You do flush them on the PC with internet connection right? Here's how I did it while I was working:
Complete packages on the machine without internet connection.
When you're done flushing, shut down the client and copy the file "buff-out.rc5" to a floppy disc.
At home start you PC with internet connection, make sure it has flushed all it's buffers and so it's buff-out irs empty.
Shut down that client and copy the file from your floppy to the client folder overwriting the old buff-out.rc5.
Now restart the client. It should say that there are x packages in the buff-out file.
You can now flush them...
Here's another tip of what could be wrong:
Make sure you update the buff-in on the PC without internet connection to let is have new packages! Or else the packages completed will be useless when flushed on the internet PC. You can see if your buff-in.rc5 file is empy on the client screen:
[Mar 15 19:24:59 UTC] 0 RC5 packets (0 work units) remain in buff-in.rc5
When it's indeed empty, copy the file from your internet PC named buff-in.rc5 to a floppy and delete it from the client folder. Else the client on this machine will work on the same packages as the PC without connection. The PC with connection will download new packages when connection is made to the internet.
Look at it this way: all packages are unique. If the same packages or empty packages are send, they will not be counted.
Hope I've explained it
Greets and goodluck!