I have consolidated some information regarding frequent issues with the most recent nightly releases. Hopefully someone finds this useful, since I've dealt with most of them myself and I see someone ask about these things daily. If any of the info here is wrong or misleading please don't hesitate to correct me (just kidding, I know you won't)
GPS
-When the option was added to use an external GPS it broke the default source to be undefined. Go to "System Settings-> Location Services-> GPS Source" and make sure "Use Internal GPS" is selected.
-Some other update changed something with the permissions of the location services settings. Uncheck and recheck all the options on the above screen to force it to ask for the proper permissions again.
4G LTE/Wireless Data
-Currently you need to reboot after installing for the first time or upgrading to a new nightly in order to get any data signal.
-Make sure you are aware of the difference between the service providers' terminology and the "real"/CM terminology (AT&T 4G is actually HSPA+, AT&T 4G LTE is actually 4G).
-Go to "System Settings->More->Mobile networks" and make sure LTE is selected under Network Mode.
-Go to "System Settings->More->Mobile networks->Access Point Names" and verify versus known good LTE APN settings.
-You may have lost your IMEI. "Check System Settings->About Phone->Status". If your IMEI shows 0 you may have to follow the instructions in the IMEI recovery thread
http://xdaforums.com/show....php?t=1801997. After restoring your IMEI you may still need to do additional steps to restore LTE. To avoid this headache back up your IMEI before you lose it using the above thread. Make sure you try just rebooting first to see if that fixes the missing IMEI.
Wi-Fi
-Some people report problems with Wi-Fi signal or connection. Try going to "System Settings->Wi-Fi->Menu/Advanced" and un-check "Avoid Poor Connections".
Volume/Sound Problems
-Audio drivers are currently a work-in-progress. Updates are still coming all the time.
-If you have no sound try turning the volume all the way down then up again for alarms, calls, notification, etc.
-Try re-selecting your ring tones in the app or clearing cache and/or data for that app.
-Call volume is known to be a bit loud now.
-There seems to be an issue with Google Now voice recognition mic volume. Try talking in to the noise cancellation mic (top).
-If your phone is not speaking Google Now results or street names in Navigation properly make sure you are using English (US) in the language settings (other languages/nationalities are currently not supported).
Camera/Gallery
-Swipe to gallery feature was "broken" by the addition of pinch to zoom. To get it to work swipe outside of image and buttons (in the grey area). **Reverted and reportedly fixed in 9/10**
-There is currently no option to store to external SD (yet).
-The built in gallery does not sync to Picasa. This is a known bug.
Battery Life
-Battery calibration is wiped after first installing or upgrading. Wait a full cycle before trusting percent reported.
-Install BBS
http://xdaforums.com/show....php?t=1179809 to track alarms and wake locks.
-Battery use after clearing caches after upgrading is high. Wait til it is finished rebuilding before gauging drain.
-Other kernels give more control over battery and performance. You can try those but don't report any other bugs here if you do.
Screen Flicker
-Has improved recently but can be seen occasionally, particularly with 3rd party keyboards or graphics intensive apps.
-Going to "System Settings->Developer Options" and choosing "Disable HW Overlays" fixes the flicker at the expense of performance.
USB Storage
-There is no UMS (Generic USB Mass Storage) mode by default on our phones. You may need to install MTP drivers or a different OS that supports it. There are apps
http://xdaforums.com/show....php?t=1711009 that allow UMS access but there are drawbacks.
-If you followed any of the procedures in the IMEI thread and did not properly revert to MTP mode you may need to do so before being able to access your storage via USB.
Home button wake
-Going to System "Settings->Performance->Processor" and increasing the minimum CPU frequency from 384 to 486 is reported to fix it.
64GB+ SD Cards
-CM will not directly support the exFAT format due to licensing restrictions
-You can format as FAT32 (with the restriction of not being able to have files over 4GB each)
-Not sure if it is supported at the moment, but in the future you should be able to format as ext (fixes the 4GB file problem, but makes the card unreadable by Windows without special tools)
Anything gapps related involving non-recommended gapps
-For example problems with text messaging when using inverted gapps
-Use recommended gapps.
Anything system related involving non-CM kernels
-Use the default kernel.
Installing/Upgrading
When updating from Nightlies MAKE SURE you are downloading the CM10 zip file. The CM9 weekly files show up in the same list.
The M flagged zip files are the same as every other nightly, except care is taken in the days/week before releasing the M edition to not introduce any new features into Nightlies that might break the system. This means that if you flash only the M files you are less likely to run into "show-stopping" bugs. After the M edition is released developers will continue adding new features to the Nightlies that may or may not result in instability.
The recommended nightly upgrade procedure should be:
-Backup/Nandroid
-Format /system (under Mounts and Storage)
-Wipe cache
-Wipe Dalvik cache (under Advanced)
-Install Nightly ROM zip
-Install gapps zip
-Reboot System
You may be able to get away with only:
-Backup/Nandroid (not technically required, but you're a crazy-pants if you don't)
-Wipe cache (It looks like dalvik-cache is included in the /cache partition on our phones - it isn't for all phones - so a /cache wipe should cover Dalvik as well. I'm no expert though, so don't take my word for it if you have problems NOT wiping Dalvik cache specifically)
-Install Nightly Rom zip
-Reboot System
Apps Force Closing/Other Strange Behaviour That Other People Are Not Reporting
-Try running Fix Permissions from recovery
-After backing up, try a Factory Reset combined with the above flashing steps to see if the error occurs on a clean system (Factory Reset does not wipe/format your SD card(s), only erases all apps and app/system data
Anything system related involving non-CM kernels
-Use the default kernel.