It's also an idea to completely reset the CS prefs (ie, trash /Library/Preferences/com.apple.logic.pro.cs , if you haven't done that yet, in case there is corruption (I had a serious issue where 10.4.2 wouldn't correctly load CS prefs from 10.3.x properly which was causing all kinds of bad behaviour).
- deleting ALL the controller assignments (Logic Pro X>Control Surfaces>Controller Assignments), and the Control surface profile (Logic Pro X>Control Surfaces>Setup), in addition to the com.apple.logic.pro.cs file (in Library/Preferences) is a good way to get back to a baseline if you're having problems.
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