Your power meter is a broadband device, I mean it is not a selective receiver. You can measure the -13 dBm level, but it does not mean that the carrier frequency which cames out from the 1st IF it is there where it should be (a relatively small frequency deviation could be enough, to measure a low level. Of course all these will also depend on the selected RBW). Try to feed from the external generator (which preferably is connected to the same reference clock as the analyzer) a 30 MHz -10dBm signal to the input of the analyzer. If this works, and you will measure a correct level, it means that your 30 MHz CAL signal is out of sync, and it is not at 30 MHz (which would be a bit strange). If this doesn't work either, than you might have a shift in the frequency of the first local oscillator. Which is possible, even if it seems locked. The phase lock of the YIG is a multi loop PLL, with several conversions, and if you change some settings in the maintenance mode, you can easily detune it (and will be locked to a shifted frequency. But if you have not changed the settings in the maintenance mode, this should not be the case). So you have to find out 2 things: if your CAL signal is sharply 30 MHz, and if your 1st LO is spot on the right frequency. They both are locked to the 10 MHz reference frequency.
Also please note: The 4.1 GHz IF is used only for the low frequency band (if I am right below 3.5 GHz). For higher frequencies it is skipped, and the IF is directly 421 MHz. Eventually, check the RF path measured level, with some RF signal in the higher bands (above 4 GHz). Just to be sure, that this path which does not use the 4.1GHz IF is working or not.