Hi, Tony C,
I only find (2) to be correctly expressed. Reference
In (1) you are comparing an accounting entry with a software, which does not make sense — either you compare entries, or softwares, but not entries with softwares. There is also some inconsisteny in comparing two new softwares. Perhaps you want to say:
1'. The journal entry you recorded in your new software does not match with the one in the old accounting software.
When some compensation is involved, you have to use another verb, for example:
3'. At the end of the financial year, your loan amount is set off against the management fee payable to you [or by you?]. (My understanding is that management fees are generally added to, not deducted from loans.)