I believe the mzClust is intended for data where you directly infused your sample to the MS; so without any chromatography. I could imagine that is why retention times gets messed up. I would just use the default "density". A ppm of 5 as you are using seems quite low. At least my instrument does not perform that good reliably.
A peak was found in some sample in the range 364.471 - 378.604. As your graph shows not all files have data at early as 364.4, therefore the fillpeaks cannot attempt to find that peak in those files and is forced to set 0. I would just ignore it.
This doesn't seem to check if the file got cut somehow if the file is still valid. I am just asking you to open the file in whatever viewer and check that the chromatogram has data in the whole retention time range as expected.
Thanks Paul. This was a Waters Premier QTOF. I think it is about five years old. I checked the first handful of scans for both functions and I get same scan times between CDF (from databridge) and mzXML (from masswolf) when viewed in mzMine. Which differences do you see?