I have a guess: In the history (right hand column) entry for your FASTQ file, click on the pencil icon to edit the attributes. Try explicitly setting the type of FASTQ, e.g. for Sanger FASTQ Galaxy uses the filetype 'fastqsanger'. This controls how the quality string is interpreted (which is important for quality trimming).
You can also specify this explicitly when you upload a file. For more about the different FASTQ quality encoding, see: http://dx.doi.org/10.1093/nar/gkp1137 http://en.wikipedia.org/wiki/FASTQ_format Peter
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