My TCP/IP may be slipping here (sadly, I left my monstrouc Cisco books either at my office or with a previous employer, and won't find out until Monday), but there is no way that your traffic can cross VLANs without going through a gateway (router). It is against The Rules. If your traffic from Subnet A is reaching Subnet B, then most likely your clients are going to your router at the edge of your network and being redirected back to the other VLAN.
This is the whole idea behind VLANs. Keep in mind what "VLAN" stands for... "VITUAL LAN", two totally separate networks that communicate with each other the same way two separate LANs do (via a gateway/router) despite sharing Layer 2 (and sometimes even Layer 1) hardware such as switches.
Do a traceroute from Subnet A to Subnet B, if you see your edge router there, that's what's happening.
Here's another question: are there domain controllers in both subnets, or are all of the DC's in one subnet?
Also, the master browsing system relies on broadcasting whole subnet, which your router most likely will not forward to the other subnet.
The Windows 2000 Server Resource Kit has some great info on this, but I'm not sure where the links are online (I looked it up in my MSDN Library), but I know you can download it, and do a search for "master browser subnet".
Hope this helps!
J.Ja