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Well, what are you reconciling to? You are looking at something that seems to be different from your data extract, so what is that thing? My trouble shooting process is to take an asset that seems to be wrong and reconcile from the report/screen data to the extract data. You have to figure out what Oracle program is involved and what kind of SQL that the program is doing and what tables it is looking at. This could be an Oracle program error. I just ran into a problem on the Payables Posted Invoice Register report, where the total did not match my extract total. Turns out the report was wrong. If I had table records with a date/time stamp value (instead of just a date stamp value) in the accounting date field for the TO ACCOUNTING DATE value in my report request selection, those records were being dropped from the report. I reported this to Oracle support and found out that there is a patch to fix the problem (happens when cancelling an invoice) and a data script to follow to fix the historical data. So you have to keep an open mind. Yes, trying to find a reconciling issue can be very painful.
My reaction is that you are looking at the right tables. There is also a FA_DISTRIBUTION_HISTORY table that you may want to look into, that links back to the FA_DEPRN_DETAIL table. Maybe your issue lies there. At least something to look at.