Merge Replication not working after 1st Sync

I am really stuck on this, if anyone has some insight into this problem
any help would appreciated...
I'll try to explain what is happening the best I can:
We have a server running Windows Advanced Server 2000 (SP4) w/ SQL
server 2000 (SP3a) (from now on Server A). I have a publication on this
machine with dynamic filters (Changing the HOST_NAME()). The
publication is sending the snapshots to another machine (desktop
machine). The Mobile agent is in the same machine as the snapshots.
The mobile application is syncing fine when hitting Server A. The sync
is done Asynchronously.
Then we have Server B. Running Windows Server 2003 (SP1) w/ SQL 2000
(SP4), same publication w/ dynamic filter however the snapshots and the
mobile agent are in this server.
The mobile application will sync the 1st time but any subsequent syncs
will not work. I check on the Replication monitor and it tells me that
the Merge was a success but the mobile application will not execute the
download table callback, it will execute the Sync callback 5 times and
not proceed in executing the download table callback.
If I change the configuration on the mobile app to point to Server A
the sync will work just fine but, if I change it back to Server B the
sync will work once then it will stop working.
Anyone have some suggestions for troubleshooting?
Update on the situation, it turns out the Sync works fine, what's
going on is that when I sync to Server A, the average sync time is 3
minutes for 2000 rows, on Server B it's taking 45 minutes to sync 1000
rows, any ideas on how to improve/troubleshoot the situation?
I also ran profiler but I have no clue what to search for. In profiler
I couln't find any issues or unless I am not looking for the right
things. Can someone tell me what I can look for in profiler if there
is anything to look for?
Specs for Server A:
CPU: 2 Pentium 3 (550 MHz each)
RAM: 3 GBs
OS: Server 2000 Advanced (SP4)
SQL 2000 SP3
Specs for Server B:
CPU: 2 Xeon Dual-Core (2.8 GHz each)
RAM: 4 GBs
OS: Server 2003 (SP1)
SQL 2000 SP4