Hello,
This has been reported before in the APDL support forum and this is a remote occurence that will hopefully be solved in the next release of Logbook Pro which has SingleSync built in. Logbook Pro orders flights first by Date of the flight, and for multiple flights (legs) on one Date, they are ordered by the order entered into Logbook Pro. A sync from APDL doesn't use this order of entry logic and therefore can get flights out of order flown on the same date.
To fix your issue you'll need to delete and re-enter the out of order flights. For example, if your flights on Date X came out as:
Flight 3
Flight 1
Flight 2
Delete and re-enter Flight 3. Since entering it last will tag an Entry time later than the others, it will sort by Date of Flight then Data Entry Date/Time.
I hope this explains the situation and possibly what you are seeing. Again, in the upcoming release this issue should be resolved.