Batch Load Skip Files

I have a strange case of file being skipped when I am doing a batch load. We are loading historical data from Dec-2010 to Aug-2012. Data is split into one file per periode(month). What happens when I run the batch load script is that all files load perfectly, expect files containing data from May (2011 & 2012) and October (2011).
I have tried to run a batch with only the files from May and October and then batch process skips completly.
Is there any setting that might have been set that can cause this behavior or anything else that I should examine. Any help or clue will be much appreciated.

File name convention is kept and the content of the file are good, if I change May-2011 to Apr-2011 and thereby load May's data into April it works just fine. Have also tried renaming Apr-2011 file to May-2011 and then it is skipped as well. Manual import of the files that are skipped works wihtout problem.
When running just the files that are being skipped, I had the script write the count of files in the batch collection and that part of the process picks up the correct number of files, in this case 3, but then they are skipped in the batch execute step.
Can this have something to do with Metadata setting in HFM? Problem started after Metadata was changed in HFM and thus we had to load all historical data again. Before that it loaded fine to May and October. At least I don't remember having this problem before.

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