S4 doesn't like Audio converters XLD, SWITCH, xACT?

Bit of a strange problem, wondered if anyone else has come across it or would see if they have the same problem.

I use XLD to convert all WAV and FLAC files to Apple Lossless. Before I installed the S4 software I never had an issue but now the software Traktor S4 or even Traktor Pro will not play any Apple Lossless files I've converted form WAV since installing the S4 software. All pre S4 install converted WAV/FLAC to Apple Lossless files play fine.

The files that won't play inside Traktor work fine in Quicktime or Itunes. But even more strange is the Apple Lossless files that don't work inside Traktor, if I convert those seemingly corrupt files to MP3 they then work fine in Traktor.
Considering AIFF files are just like WAV I thought I'd just convert from AIFF instead, but the same problem happened

In the the exact order of what I've done

WAV convert to Apple Lossless = file didn't work, convert to MP3 = file worked, convert to Apple Lossless = file worked

WAV convert to AIFF = file worked, convert to Apple Lossless = file didn't work.

At first I thought this to be a XLD bug, but I've tried the same thing with xACT and still the same issue.

So is there any S4 owners who use XLD or xACT who could help/check if there having the same problem with Apple Lossless files.