I've had this problem for a long while now, and have posted here multiple times with no solution found.
I just googled again, and finally found another person who seems to have the same problem...
Problem: Audio File Timing Error after Merge Caused by Low Latency Button
System: Logic 9.1.1 under OSX 10.5.8 on MacBook
Description: When merging two audio files there is sometimes a timing shift on the new merged file, which on my system was a delay of about 2400 samples (about 57 ms at 44.1 kHz). I usually noticed this during swipe editing with "Flatten and Merge" of audio takes. Once in this state, any bounce-in-place or merge operations will be delayed and the only way to get out of this state so that merge would work correctly was to restart Logic.
The effect is a bit subtle and might not be noticeable depending on the program material and the listener. However, it is certainly large enough to wreck a groove.
Neither Rounik nor I could find this reported anywhere.
Work-around: Since I really like the swipe editor (even my vocals can be made to sound decent) I spent a lot of time chasing this to determine what triggers this erroneous state. After toggling every conceivable button and preference that might be remotely related I finally did stumble on the trigger:
If the Low Latency button is enabled (orange), then the timing error will occur for both bounce in place and merge operations.
It just so happens that when swipe editing fresh audio takes with flatten and merge operations, it is likely that the low-latency button is enabled for recording.
I sent a description of this "smoking gun" to Apple support, and it is probably a 5-minute fix for them. Hopefully we will see it soon.
In the mean time beware of this since the effect may not be blatantly obvious, but certainly does kill a groove.
Please, please fix this problem!!! It's so subtle that I won't notice it until it's too late, and it will really screw some things up.