We all know P6 is not good at reporting so maybe you will not be able to get the report for calendar exceptions. In such case print the report from P3 and compare within P6 calendar views, remember exceptions can change on a yearly basis while others are repeated.
I believe it is on calendars that most such transfer issues are originated. Next suspect would be "lag" values as converted when using, on P3, "day" as the planning unit.
We tried before to export P3 files into P3e a prior version of P6 and they behaved differently we ended using P6 to draw bar charts and P3 and SureTrak to evaluate claims. Beware that if you click update on P6 it will recompute the values you got on P3 so in order to keep them use P6 as a drawing software, do not run update on your transferred files.
Although we had a preference of P3 over P3e(enterprise)/P6 we immediately found P3 cannot handle large Portfolios. We ended up with a version we liked that cannot handle large portfolios and a version we did not liked but able to draw large Gantt Charts. Because the jobs were stand alone job we had no real need of Portfolio functionality at the individual job level.
We also found P6 although could handle Portfolios could not deal with our main need for Portfolio functionality, to consider Financial Constraints in our "What-if" Scheduling for possible future jobs.
The following link can be of some help:
http://www.drmcnatty.com/publications/enewsletter/febtechtip.pdf
Cordially,
Rafael