You're not using a power mike on this radio are you?
It's fairly common for an amplifier to 'bleed' the circuits in a power mike, creating a feedback squeal on the air.
Even more basic, the quality of the connection inside the connectors on your coax and coax jumpers is a big deal. Unless the shield braid is soldered, this can cause a problem. Sometimes a barefoot radio will work okay with coax plugs that are grounded poorly inside. But putting an amplifier in line with them causes trouble.
Do you have a SWR meter in line with the antenna? Any time you have an amplifier in line, you need a RF wattmeter in line with the antenna.
High SWR on the antenna can cause headaches, too.
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