Had the same issue with these feet as well. My bf and I spent 6 hours in Vunkerl one night, 8 hour the next... the following day we went to try again and got them in the first goddamn chest that dropped. -.- We both only had two gold box abyssites (abyssite of destiny), had amber killed one ephemeral murex and pearl on a few VNMs.
My definite suggestion is keep your amber low, don't get it to the point you're getting big boxes. Just enough to get the small boxes to drop with synthesis materials and scrolls in them. Seems to me the lowest tier small boxes have various seal NM triggers/temp items, then synth mats/scrolls/shoes with stronger amber in small boxes, and key item triggers/higher quality temp items in the largest boxes. Augmented items seem to be thrown in there randomly and the augments just get better the more amber you have. I've seen shoes in large boxes as well as higher quality synth mats (khroma ores/o. ingots etc.) but it's much more common to be a key item or temp items like revitalizers once they all start dropping as big chests. I've seen 2-3 feet load in one small box on the first gold chest to drop, multiple times. Try building up pearl on a couple VNMs, amber kill one murex and start farming, I prefered mobs that don't give ruby so you can weapon skill kill and not overpower your amber light with ruby. I think the only mobs that don't give ruby in Vunkerl are murexes and bats, possibly tigers as well. You could azure kill an ephemeral murex or two as well if you want to go for time extensions but if you keep amber your strongest light then you should get more gold boxes. Of course you'll still get red and blue without farming any azure or ruby due to abyssites, but gold should be most common.
Keep in mind, I'm only speaking from my personal experiences and this is what worked for me. We saw them drop within 30 minutes this way, and most of that 30 minutes was spent chasing down VNMs for pearl. And for what it's worth we finally got the ninja feet off of the bat trios. We farmed peapuks the first night and got SMN DRG SCH SAM and 2 PUP, murexes the second night and we only got 4 SAM and 1 SMN off of a random marid as we were leaving. I personally doubt mob type has anything to do with it but who can say for sure. These feet were definitely a ***, good luck! Sorry for the wall-o-text.