(Sorry to resurrect old-ish topic, but I think it's better to continue here than to make a new one.)
Same problem here, except the only custom thing I've ever run on this phone, is apps from market. I'm running SPB Shell 3D (legal version, but not through Android Market but the other thing SPB was selling their programs through... Handango? Not that it matters.)
The phone has been running ALMOST perfectly since day one. I can only remember two occasions that the phone was in "no reception" mode (the O with slash through it) and toggling Flight Mode on and then off fixed it both times before.
However, yesterday I noticed the icon again, thought nothing of it and switched Flight Mode on. It never went back on again. Googling the problem I bumped into the imei/baseband thing and sure as not, when checking my phone's data there is "unknown" in the baseband version and IMEI is empty.
Trying to enter Mobile Networks settings results in "insert sim" notification.
The phone is (OS-wise) completely stock, I think the only thing I have ever done to it since then was to update it to 2.3.5 via KIES when it became available.
Phone is unbranded and not simlocked and never was. The only alterations are the aforementioned SPB Shell 3D and WidgetLocker. And of course a bunch of "normal" apps, games and such.
I placed a call (which went unanswered for all it matters), then after a short while (five minutes or so) noticed the "no reception" -icon. Then all went to hell.
Tried with three different SIM cards, none work on this phone, all work on other phones. Currently SIM working in Galaxy Gio.
I plan to take the phone to repairs under warranty, I'll let you know what they say and what happens to the phone if I remember.
Sony Xperia Z Ultra (Sony 4.3)
HTC One (HTC 4.3)
Apple iPhone 5 (iOS 7, Jailbroken)
Samsung Galaxy Tab 7.7 (Samsung 4.0.4)
Nokia Lumia 710 (Rataplan v5.0 WP7.8)
Apple iPad (iOS 7)
Misc: Samsung Galaxy Tab, HTC Hero, XCover