Default Integrate updates on system with titanium backup

Since i have the nexus 5 and android 4.4 I have problems with the apps i integrate into the system with titanium backup. Why this? is because they are deodexed and system is odex? no problem with 4.3 jelly bean. Thanks

: Nokia 6510 -> Sony Ericsson Z600 -> Sony Ericsson W880 -> Sony Ericsson W980 -> Sony Ericsson Xperia Arc -> Google Nexus 5 32GB