I happen to have the BEFSX41 - right now I have two WinXP machines hooked up to it... one in the DMZ port (#4?) and one in the next port (#3?) (or DMZ #1 and regular #2, can't remember now cuz I'm at work) both using Linksys NIC's.
Had the exact same problem!! The pc in the DMZ port (I know, I know, but DMZ is never enabled on my box!!) worked fine but as soon as I plugged in a second pc to ANY port, the whole setup would pork out on me. Like you said, sometimes both would work for a bit, sometimes they wouldn't. Ended up powercycling the router 3-4 times a week (for about a week until I got fed up!!)
I had quite a bit of detailed port forwarding and port triggering going on but when I upgraded the Firmware, NO settings were lost and it DID resolve the issue.
In speaking with Linksys support (prior to the update) they mentioned numerous problems in general with the BEFSR41 and had NO plans to release new firmware or attempt to resolve the issue.
Just food for thought.....
(Oh, and I'd spend the $15 go with the SX41 instead of the SR41)