If you switch the amp off and attach a 50 ohm load to ANTENNA 1 and the rig to the RADIO, does the rig see a low SWR?
If not, there's something wrong with the input jack, maybe the center pin is not soldered (it's happened before).
If the SWR is low but only goes high when you key the amp, then the problem is most likely the coax jumper going from the back panel to the LPF board or going from the LPT to the amp deck.
The problem could also be T1 on the amp deck, it the core was backwards you might see high SWR.
Also, be very careful using a 100W radio with this amp. If you inadvertently hit it with more than 25W of RF the protection circuitry can't react fast enough to prevent damage.
73,
Jim WA2EUJ