I’m guessing the clip to which you are applying Corner Pin Studio is trimmed on the front? It appears that when you pipe in a secondary matte input in Resolve, it assumes that secondary input starts at the same time as the original, untrimmed main tack. So if you trimmed two seconds off the front of the main track, then it automatically trims two seconds off the matte track as well. Also it appears to automatically loop if the secondary matte input is shorter than the main track (ignoring all trim). It is unclear without more research whether this is something we can control as a plugin. Perhaps we could add a “time offset” slider for the secondary input to account for this, but even that would be a kludgy workflow.
Does this seem to explain the situation you are seeing? If not, then would you be able to share a project file with us? If this does explain it, then the workarounds I can envision would be padding the front of the secondary matte track by the amount of the trim. Or pre-rendering the main track in shortened, trimmed form so that no front trim is required on the copy where Corner Pin Studio is applied.