It is the Check function which is throwing the error. Try using:
ParallelDo[
Do[Quiet@Check[{i[[1]], j[[1]],
FindGeometricTransform[i[[2]], j[[2]],
Transformation -> "Translation"]}, {i[[1]], j[[1]], err}], {i,
files}],
{j, files}]
If you leave off the Print command, it will silence all kernel outputs, and also speed up your computation (I'm sure other's could expound on this, but displaying outputs while running loops tends to slow things down). If you want to monitor the output of a parallel computation while it's running, check this SO post.
Edit Just realized that putting Quiet on Check kills the whole point of your computation. I think it would be best if you just do the calculation as a Table and extract the data at the end:
Quiet@ParallelTable[{i[[1]], j[[1]],
Quiet[FindGeometricTransform[i[[2]], j[[2]],
Transformation -> "Translation"]]}, {i, files}, {j, files}];
I'm not completely sure why I need both of those Quiet commands, but it seems to need it.
Quiet[]? – 0x4A4D♦ Feb 2 '12 at 10:59