well the first question i have is, which SWR are you talking about?
when you add an amp in line after your radio, you actually introduce an additional "load" that is different from the antenna "load".
let's say you have a cobra 29LTD that has a built in SWR meter.
you've checked it against a good external SWR meter and you know it to relatively accurate.
so, you connect your antenna to the 29LTD and you check your SWR.
let's just say you read a 1.3:1. great!
your antenna is tuned well.
now, you put an amp in between the 29LTD and your antenna.
When the amp is on, the radio is no longer reading the SWR of the antenna.
it is reading the SWR of the input stage of your amplifier.
so moving ahead with our scenario of a known 1.3 SWR without the amp in line.
now, with the amp on, you key the mic on the 29LTD and check the SWR again.
now it reads 2.5:1.
This is not a problem with your antenna, this is a problem with the input circuit of your amp.
some amps make this an adjustable setting, but most do not.
this is why you see a lot of people taking their radios and amps to techs asking them to "marry them" or "match them".
the tech is going to tune the input circuit of the amp to as close as they can get to a 1.1:1 SWR from the radio into the amp.
this way, most of the power coming out of the radio goes into the amp and is not reflected back into the radio.
to actually test your SWR at the antenna when using an amp, you have to add an SWR meter AFTER the amp.
if you tune your antenna to a 1.3 and then with an amp in line and on, the SWR measured after the amp rises by more than a few tenths, you either have a problem with the output stage of the amp or the antenna itself.
hope that helps.
LC