Passive Respec Sometimes Reverts Half My Changes

Currently doing a large respec, ~20 net nodes changed and some changes at beginning of the tree so have to reshuffle along the way.

I have just attempted the same respec 3 times in a row, all three times my tree has come out VERY different, my gold total is not the same as the tooltip indicated, and after one of the respecs my passive tree looked different when viewing via the respec window and via the P hotkey (no it wasn't from weapon swap.)

I have tried restarting the game, that fixed the mismatch between my passive tree and what was shown on the respec window, and it showed the respec window passives.

No idea what would have caused this obviously, the first respec I did I hit my F4 key which has a chat macro for /tradewith @last, that seemed to confirm the allocation (since the first key is enter) but I closed and reopened the passive respec window and it was not confirmed.

Just tried again, here there the pics: https://imgur.com/a/3QEYJQz
In this case two nodes reappeared after confirming. In previous attempts:
- The left part of the starting diamond reappeared every time I tried
- The right part of the starting diamond disappeared the first respec attempt
- The middle column reappeared every time except the time I took the screenshot (I am reallocating the remaining nodes in the column to weapon set 2 btw, so maybe this has to do with the order the tree validates nodes?)
- The travel nodes in the top left that let me de-allocate the middle column disappeared every time until I took this screenshot.

Basically had to do my respec in parts, and since I had to de-allocate nodes at the end of the tree so that it would let me redo the starting section, when those came out de-allocated form a respec I was essentially paying extra gold that wouldn't have paid if the respec worked. All in all initial respec cost said I would have 80k left over and I have 50k.