Proffits dissapearing from pick up window.
Make sure your mail is emptied out. Yes, I know it sounds odd, but having a full mailbox can cause items/gold from the TP to back up in the queue. It may take a few hours for the items/gold to show up, as well. It’s worth a try.
Coins do not appear in the pickup window if the windows is already full to capacity with other items. Collect everything waiting in the TP, and you may find your coins on a page 2 or 3
//Portable Corpse
Thank you for your replies and suggestions.
@ Inculpatus – I only had 3 mails, but deleted them anyway. This unfortunately did not help.
@ Yamagawa – THIS WAS IT! I have never noticed this before.
It still seems odd but perhaps that is because the buy orders screen and most other screens show as “pages”, but the filled orders “pick-up” screen seems one continuous scroll down page. After accepting a few hundred buy orders, the missing gold started showing up a bit here and a bit there. Thank you both for your help! 
I’m glad you found the issue and received your gold. =)