TargetLynx Won't Always Integrate?

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I'm running into an issue where when I process my entire LC/MS run, my analyte will not integrate. I've verified that it's looking for the right retention time, that the peaks are actually there, attempted to adjust a few additional parameters, but it doesn't seem to help. However, when I just select my standard points, TargetLynx has no issue integrating all the data. I'm sure that there's a fix I'm overlooking, does anyone have any idea what could cause this?