Hi John,
there are several ways to update the analysis view, depending on the setup and on performance considerations. One is not to update the analysis view on every posting. This can be set up in the analysis view card. I would guess that this is the most probable cause for a difference. The remedy is to start "Update Analysis views" by hand before you do the analysis.
There are other possible issues: Often there is a customization to edit dimensions in posted ledger entries. This can also be a cause for deviating analysis views. The analysis by dimensions functionality itself is quite stable.
with best regards
Jens