Hi Christopher,
Do you use WCCP or Inline interfaces?
In both cases, I would take a capture directly on the WAE with the tethereal command to see the packet before and after it is handled by the WAE.
Something like this should get you what you are looknig for:
tethereal -s 1600 -w optionscap -i -f "host 10.107.160.238 and host 64.46.224.78"
If you use inline, you'll need to set this up from two CLI, one for the WAN side and one for the LAN side.
This should show you exactly the changes WAAS is doing to your TCP options as we can then compare the SYN before and after it is handled.
Regards,
Nicolas