If the GL posting batch does not balance to the depreciation that was run in Fixed Assets, there could be several reasons to explain this. 

Usually we find there are accounts that wash each other in the Account Group setup.  If the same account is listed twice, the amounts will offset each other and the batch would leave those out.    To verify, you can go to Inquiry|Fixed Assets|Financial Detail and look at the asset in question.  Go to the FA period and click on a line from the period in question.  Here you can drill back on the Amount link to see more details.  It should show the GL posting account and the GL Posting batch that it was included in.  Then check the other side of the entry to see what account/batch is listed.  Usually all the entries you were expecting are listed and in the correct GL batch.  But if some offset each other, the batch would be off by that amount.

Note:  You would also see all the entries that are included in the batch by running the below statement in SQL Server Management Studio against the company database:

 select * from FA00902 where GLINTBTCHNUM = 'FATRX000000XX'
--enter the appropriate batch number in the script above. The example shows is the default format and you should edit the XX placeholders.

I hope these steps are helpful to you to assist you in verifying that the GL posting batch is correct, even though the amount may not be what you were expecting.

Regards,

Cheryl Waswick | Sr. Support Engineer | Microsoft Dynamics GP Support