I ran a test that Rich suggested. Specifically I used an HP signal generator to produce test signals of -50dBm to -90dBm. The received RSSI at the AX5043 is within 1 - 2dB. This suggests that the antenna connection, matching circuitry and filter are all working. The signal is getting to the chip as expected.
Tuning the signal up/down does not improve things. So the chip does seem to be on the right frequency. I also ran the "test freq" function (after modifying it to work with the AX25 code). It transmits on the receive frequency, and it seems to be correct within a kHz or so.
So this leaves us, as expected, with some sort of register setup issue. Given it is worse on 2m than 70cm it is perhaps a bandwidth or frequency acquisition issue.
73 Chris