Ah, the eternal dilemma; a shortage and it always seems to fall on the parts manager; the "accountants" are "never" wrong. Humbug!
I would suggest two things that would insure what I call "count integrity" which, simply put is prove your are right and make them prove you are wrong; it seldom fails.
1. Do a perpetual on the fastest moving 3-500 parts on a monthly basis. Reynolds has a great "Piece Sales Ranking Report" that will give you the numbers to count. You can also run the report with the generator and sort the selected numbers by bin location; ergo: a count sheet. When you prove the count in the bin matches the count on the shelf, your inventory is good.
2. Using a monthly reconciliation form; A copy can be obtained for free from
www.partsconsulting.com as a download. Jeff Sacks made this for me a long time ago; it is still applicable today. It's not for sale, its free for the taking.
Do the reconciliation monthly. With the perpetual and reconciliation done, if there is still a discrepancy It may very will be in accounting and the coding they do. If you buy 5 and sell 3 and there are 2 in the bin; You are RIGHT; end of line.
Mike Nicholes
Having said that. You do need, and it looks like you did, sit down with the accountant, especailly the accounts payable clerks and make sure that 1) you are coding invoices to the right account and 2) they are inputing the data YOU posted to the right account.
Curious: Who does the annual? Outside firms are great if you are flush with money. It is the CPA's that want an "unbiased" version of what it is your have. the trouble is that most of the outside firms make one serious error; they net the minus adjustment against the plus adjustments and come up with a "NET"! Is somebody kidding? No overage in the word ever offset a shortage; especailly if it happens to different part numbers. the "discovery" of an engine does not give you 'dime one' to replace so called shortages. overages are only caused by paper flow issues. Shortages MIGHT, and I emphasize "MIGHT" be theft; but in all my experience only 5% of less of all shortages were theft.
Clean your own stable first then go after theirs.