Do you have a pair of running sandals? Or running shoes that lace well down into the forefoot? Maybe try running in them to see if the problem shows up even in a more open toebox (mind you, a sandal doesn't really have a toebox, but you know what I mean.)
No, I wish I did. I have my other running shoes and they felt fine but apparently they were too supportive and I didn't need a supportive shoe and they were causing my knees to hurt.

Since changing to these shoes my knees have been great but I've had this toe issue. It's really hard to get it all fine tuned, isn't it!

Also, pull out the other shoes that cause this problem and compare them to the shoes that don't. Pay close attention to the width and depth of the various toeboxes.
I think you may be on to something. It also might be that these shoes just aren't quite long enough (even though I thought they were) and when I run my foot slides upward??? I'm not sure.

Sometimes it's fun to stand on a piece of paper and trace your bare foot, cut the tracing out, and hold it up to the underside of the shoes that irritate your toes. It can sometimes be an eye-opener, especially if the tracing is wider than the shoe.
I'm going to try that!