I have the same issue on a brand new TI2 Desktop. I did upgrade it to the latest firmware using an old iMac. However I still have the issue, so I don’t think upgrading will help…
How old is your unit?
Can you try playing the built-in demosong and keep it playing over and over on a loop?
I noticed on my unit when I play the demo song and leave it playing, often times I get the same issue, a loud constant beep… or a short beep and then it goes completely silent and sometimes even the knobs stop responding completely.
I have contacted my retailer and Access support, hope to find out if this is just a quirk or serious hardware issue, just like you. 
It seems there have been more users with this issue if you search online, for example user ZX81 on this forum.