The only easy way, (relative term), would be through VBA I think, (unless you want to export the sheets to another format, eg CSV, and use another program).
1) Grab amount entry from spreadsheet A, (X)
2) Look for a matching amount entry in spreadsheet B, (Y)
3) If X = Y then check to see if the time between them is less than 2 minutes
4) If it is, mark both entries as OK and go back to step 1.
5) If time doesn't match, go back to step 2.
6) If at the end of all values in spreadsheet B you haven't found a suitable match then flag the entry in spreadsheet A and go to step 1 until you've cycled through all entries in spreadsheet A.
The problem with that is if multiple entries occur within the space of a couple of minutes with the same amount.
It would probably make things a lot easier if you could synchronise the time between the two systems, eg. install a NTP server on one and have the other set its time from it.