Large Thumping noise

That woofer excursion thump is very likely subsonic bass distortion. There are warps in vinyl records that create the stylus to pick up a LONG signal and your amp recreates it, sending the signal to the speaker. The amp controls the movement of the speaker magnet - hence the distortion and "thump" as the woofer magnet reaches it's travel limit. That is MURDER to speakers and draws LARGE current to your amp. Both damaging to equipment.
You're not dropping your tonearm on the vinyl suddently are you?

the interaction between the amp and the speakers causes this. many pre's used to have subsonic filter switches to eliminate this. a good match of amp/speakers should not be doing this.

Could be the table is not isolated properly.