The most damaged components in a spectrum analyser are the first mixer, pre-amplifier and, in extreme cases, the input attenuator. The input socket centre contact is also a potential victim of abuse.
Mixer death is usually accompanied by a larger signal loss than you are seeing. A MMIC gain stage at the input of the analyser would be a possibility as if can continue to operate but with no amplification. You then effectively lose its stage gain but all other functions such as the attenuator and mixer work normally.
One of the greatest errors that some spectrum analysers make is to connect the RF input to an open circuit type antenna. ESD and static present themselves to the sensitive front end electronics and cause al manner of damage. It is a good idea to always have a 10dB attached to the input of an analyser and only removing it when you are absolutely sure it is safe to do so. Many Spectrum Analysers need a button sequence to select 0dB input attenuation for just this reason. The manufacturer likes to keep a pad in circuit to protect the sensitive RF stages that follow.
As to a software fault, sorry, I don't buy that idea. It would initiate a recall from Instek and much talk in the industry.
My advice would be to carefully investigate the RF front end circuit.... they are usually pretty easy to understand and are often laid out in a linear fashion with interstage screening, stripline interconnects and 'weird' pcb filters
If you get lost, just post a picture and I may be able to assist in identification of possible culprits.
Aurora
Additional comment. The unit has front end protection..... normally a couple of fast diodes and a pad. Worth checking that this has not been destroyed.
On many spectrum analysers you can see the 'Zero' marker at 0MHz (its actually the the first L.O).
Is that at the correct amplitude ? Issues here can mean mixer damage.
Also, check your noise floor. Is it still within spec ?