Computer Analysis Annotations Misleading

I am not sure what engine chess.com is using for its analysis, but having submitted a number of my games for review, I have noticed a trend.

The engine seems to be very liberal in assigning inaccuracies (?!).  When I later review my games with Fritz or Houdini, often the "Inaccuracy" is merely the engine's 2nd or 3rd choice, and the change in score as a result of this selection is rather marginal, (often less then .30). 

Similarly, what chess.com's analysis calls a mistake (?) often is more of dubious move according to Houdini/Fritz.

I think that whatever parameters chess.com is using in its computer analysis should be reviewed, as it might be giving players the impression that they are playing very poorly, when in fact this is not the case.

I think their engine is a trade secret for obvious reasons, though Crafty is famously used by different chess sites (I know Chessgames.com uses it), but it could be Shredder or Hiarcs for all we know too (two excellent engines though the newest Hiarcs isn't on the Fritz interface =(  )

I believe the engine was programmed by member(s) of staff b/c of a thank you I received for playing against the computer a lot in the live chess.