Small Business not always getting paid

I'm having a very similar problem to the one you're describing. I traced the problem to a mod I'm running and very much need in the game. It needs updating and I tried to alert the mod author to it.  With some experimentation, I found this happen much less often with PCs (the characters under my control) as the Tattoo artist, and more often with NPCs (hired characters I do not control) as the artist. Also, the end of day financial report is not always accurate. I would not use it to calculate how much money your business actually made. Since I don't have time to babysit the NPCs I hired, I got rid of them and just use my PCs to do the work, and if a payment gets missed, I record it and cheat the money in after the business is closed. It's the only work around I can think of.