(Solved) Strange timeout issues.

[c0urier]

Hi folks,

I've come a cross a problem I can't seem to figure out by myself "once again". We have previously been running pfsense 1.2.3 without problems but after we upgraded to 2.0-RC* we have started to see some strange timeout issues from our primary site to the secondary site (And only those two affected).
The timeouts come randomly if the primary pfsense box has been running for more then 10-20 minutes. As far as I have tested it's only SSH, any RDP protocol and our game servers affected. It's only our primary site that gets the timeouts no one else. If the pfsense box at the primary location is rebooted everything works fine again for 10-20 minutes then the timeouts are back on the mentioned protocols. If I make the second pfsense box pingable, and ping while the timeout occur on the different services the pings are not affected. I've reinstalled both boxes and made all port forwards for Game servers, SSH etc but this haven't helped on the problem.
I have been out buying new network cards for both sites since they were running Realtek chipsets, so they have been switched to two Intel 8492MT PRO/1000 MT Dual Port Server Network Adapter. I'd really like some help troubleshooting this issue, and I am in no way a guru when it comes to firewalls/routers. So all help is greatly appreciated. If it's not clear what I am writing please let me know and I'll try to explain it better.

Info:
Primary pfsense box:
2.0-RC3 (amd64) - built on Tue Aug 2 22:54:59 EDT 2011
Intel(R) Atom(TM) CPU D510 @ 1.66GHz
4 GB memory
1x Intel 8492MT PRO/1000 MT Dual Port Server Network Adapter (For LAN/WAN)
Internet: LAN connection to a local fiber provider. 100/100Mbit (Public static IP)

Secondary pfsense box:
2.0-RC3 (amd64) - built on Tue Aug 2 22:54:59 EDT 2011
Intel(R) Atom(TM) CPU 230 @ 1.60GHz
4 GB memory
1x Intel 8492MT PRO/1000 MT Dual Port Server Network Adapter (For LAN/WAN)
Internet: LAN connection to a local fiber provider. 30/30Mbit (Public dynamic IP)

** Edit:
Seems to be an ISP related issue, tried taking a cable directly connected to a PC around the pfsense box, same lag issues. Very strange since it's the same ISP in both ends. Just bad luck it occured when we switched to pfsense 2.0.

[c0urier]

I wrote a mail to my ISP yesterday. And today I upgraded both pfsense installtions to: 2.0-RC3 (amd64) built on Fri Aug 5 20:24:40 EDT 2011

And the problem seems to be gone. So I wonder if the problem was solved by the pfsense upgrade or my ISP. Though my ISP don't answer support tickets during the night and in weekends. Could someone tell me what has changed from:
2.0-RC3 (amd64) - built on Tue Aug 2 22:54:59 EDT 2011
to
2.0-RC3 (amd64) built on Fri Aug 5 20:24:40 EDT 2011?

**Edit: Nevermind, the problem came back when I closed the SSH session from Site one's pfsense to Site two's pfsense and further on to the server. Odd.