If you're doing IPSec over UDP/TCP then you shouldn't see these protocols, as they'll be inside a UDP/TCP packet.
If you're not doing UDP/TCP encapsulation, you should still be able to build a tunnel to whatever it is you're connecting to, cause this is all done with ISAKMP (UDP 500). If these are being blocked by your ISP, you then won't be able to ping or transfer any data over that tunnel, cause this is all done with protocol 50 and 51 packets. Of course, these are also not handled by a lot of PAT devices, so it may not be that your ISP is blocking it, but rather you're being PAT'd somewhere and this device is dropping them. If you have a valid global IP address though, you probably aren't being PAT'd.