There is a BIG difference between 'muffled' and 'quiet'. In a normally operating system, the level you record at can be a range of different levels - some leave it high, some low - but everyone runs at a sensible level so their recordings are not noisy. - as in hissy!
If you turn a condenser mic 180 degrees around, it gets muffled as the most sensitive side is pointing the wrong way. If you use an SM58 very close in, it can sound muffled because there's lots of bass and little treble. Muffled, to us means lacking in HF in most examples. That's why hearing it is so important - loads of us will know what's wrong when we hear it.
One question - when you are listening on the headphones to the live output - is that muffled too? is there a mic position where it gets'unmuffled'. Your DAW is simply recording what it is given.
Level can be fiddled with, and if you are heaving to turn the gain up really a long way on more than one mic, then it suggests that you have a physical fault - BOTH faulty, a rare thing, or a cable fault, more common, but you have nice coloured ones which suggest they're unlikely to be both faulty - or the one shared component - the interface. I assume it's the same on both input channels if you record in stereo with two mics at the same time?
We need more factual info.
