When it places bets below minimum allowed stake by Betfair which is $5 it first has to place a back bet for $5 at 1000. It then changes the stake to $5 plus your actual stake which creates an additional bet for your required stake. It then cancels the $5 bet and changes the odds to your required odds. It must be failing at the second step leaving the bets at 1000. Usually the cause is exceeded exposure, but it sounds like you have sufficient funds.
Can you send the diagnostic log to
admin@gruss-software.co.uk
It is named BA_Diagnostix.txt and is located in c:\temp\Betting Assistant Logs