BOVPN strange issue

Hi all,
I've 2 sites:
the first has an XTM 330 12.1.3U2 with 3 external lines (1 line dedicated for VPN with the other site)
the second one has a T30 12.1.3 with one external line, they use the VPN to connect to the primary site with RDP and with some other services (MFP scan to mail and scan to folder)
there is a "classic" BOVPN ipsec with those sites.
The issue is that somethimes the customer call because have issues with RDP, they cannot connect to the hosts, the MFP stop sendin mail etc, but they can ping the servers to the other side with decent ping times.
If I see the SMTP logs I can see the communication coming there is the first handshake but then timeout occours...
I've tried to rekey the vpn and reboot both fireboxes without resolving.
If I switch to another line at the main site it resolve the issue, but again after sometimes the issue come back and I have to re-switch to another line and maybe it is resolved.
This things is driving me crazy.
The last resort is tring to switch to a TLS based Bovpn.
Any Ideas how to troubleshoot to identify the key issue?
Thanks
Gabriele