Thanks for the reply. It's the frame after the cut. I could have put the frame before the cut instead I suppose but same difference. Basically, one capture style interlaces that cut, the other keeps it clean for the two shots (and lowers everything a scanline).
Regarding VCR: It is a JVC HR-S9911U -- one of the top consumer models made -- so it's no slouch in the VCR department, and mine is in very good condition. No indications of anything wonky with it.
Regarding tapes: Every single tape of the dozens I've tried results in this. Some of them are barely played pre-records, so it's not a tape problem I'm sure.
The cable (in case that's what you might suggest next) is a $150 S-VHS Monster cable, going straight from the VCR to the PDI card. So I doubt it's that either (especially as I've used more standard cables also and no difference).
In a narrowing down fashion, this leads me to thinkin' that perhaps it's my PDI card drivers? Do you still have a copy of the sweetspot drivers you used to do a compare? This is what I used/installed: sweetspot_wdm_driver.exe, the file size (in properties) listed as 524,288 bytes.
Edit: While I had confidence it was not my JVC9911U that's the prob, for kicks I hooked up my "cheap" VCR and did a bunch of captures with that. Interesting find... I did 9 caps in a row of the same segment above, did each by hitting f6 then after three or four seconds hit ESC, back-scanned, then hit f6...ESC, scanned back the few seconds, repeated this 9 times to get my nine capture files. All nine came out exactly the same way (like the second pic above). "Culprit found!" I thought, "'Tis my beloved 9911U that's the problem!" However, I did some more caps for kicks, this time hitting stop on the VCR and rewinding after each (rather than just back-scanning) and I got the same problem I've been having, half the caps like the first pic above and half like the second. Note that I never turned the VCR off, nor did I exit the "capture" screen in VDub for these. Whatever this change is, hitting the "Stop" button (or "Play"?) on the VCR is all it takes to allow it to happen. Curious.