The sock/insulation stuck in the reflex port of a speaker is meant to be used when you position the speakers right up to a wall.
As I understand it (probably incorrectly) the port is tuned so small speakers can sound 'bigger' by using the wall behind them to reinforce the sound. To do this the speakers should be a certain distance from the wall. If you have to put them a lot closer than this, I think you stuck the bung in the port to stop it working as otherwise it would be over the top. Sorry, not the correct terminology but the point is there somewhere.
My TDL RTLIIs are good because they have some kind of horn thing inside that provides good bass performance from compact floorstanders and as the ports are at the front you can stick them as close to the wall as you want.
Best advice I reckon is to double check your speakers are wired in phase. I had a mate who spent an absolute fortune on a Micromega amp & a cd player. I think he had some expensive Mission speakers too.
He thought it sounded amazing & had been using it for a month or so. I went round there & thought it sounded completely pony…..turned it all off, checked the speaker cables & swapped them around……BOOM……I made his stereo sound 10x better for free!! He was quite embarassed.