iTunes match error

I have just subscribed to iTunes match and am in the process of matching/uploading my entire catalogue to the cloud. It is quite a large library (nearly 12000 songs) so is taking a while.

I'm getting quite a few error files that aren't matching/uploading. For example, most of the Sgt Pepper album is returning an error message. It's encoded as Apple Lossless. Therefore I tried creating AAC versions of it a lower bitrate, but when I try and upload those files they just return a 'duplicate' message as if they're already in the iCloud library (which they aren't because when I try and access those songs from my iPhone they're all greyed out.)

Does anyone know a good workaround for getting these problematic files into the iCloud music library?

Any advice much appreciated thanks in advance.