If you decrypt the update and unzip you can see if any part of it is an incremental update (instead of a full update) which might be a conflict if you modified something. If any of the "patch" files (vs. "new" files) are not zero, then it's incremental. Or you can look at META-INF\com\google\android\updater-script to see if it says things like:
Code:
ui_print("Patching system image unconditionally...");
The most proactive way to investigate this would be to take it to recovery and manually install from there over ADB. That way you get the real log.