A tweaked radio can cause this, if the wrong tuning slugs on the main circuit board got molested.
I would apply the cheapest and best tool on hand, the calibrated eyeball. Pull the heat sink off the back and then unbolt the tin shield cover from the linear. When things go wrong in that amplifier, something nearly always gets scorched badly enough to spot easily.
That amplifier will tolerate almost no SWR at all. If someone has mistreated it, the evidence will be visible.
It's possible to pull a plug and put the amplifier on standby. This would tell you how much power the radio has to drive the amplifier. A weak radio circuit board will hold back power even if the linear is perfect.
So far you have a chicken-and-egg puzzle to solve first, deciding whether to blame the amplifier, or the barefoot radio's performance.
Thought I had a picture of the plug you pull to disable the amplifier and make the radio barefoot. I'll keep looking.
73