My husband is a dentist and has all sorts of random dental products in our house. One product in particular caught my eye and my cup life has never been the same since. They are called proxabrushes - the brand we have is called "Go Betweens" but I am sure any other brand of proxabrushes would work just fine. They are teeny tiny brushes that are supposed to be used for cleaning very small spaces between teeth, dentures, and the like. They have antibacterial bristles, can be used over again (up to a point), and are pretty inexpensive (2-3 USD). I thought maybe they would be really good for cleaning the holes in my cups and decided to use them on my next cycle. I did and they worked. Amazingly well.
Here's what they look like: (from left to right - brush cover, brush, packaging)
They fit perfectly into the holes and make cleaning them very, very easy.
They are very soft, almost like a tiny pipe cleaner. I lather up my cup wash (a castile soap mixture I made) in my hands and put a tiny bit of it on the bristles of the proxabrush and just work the brush in and out of each of the holes while I'm cleaning the rest of the cup. When I rinse it off, the cup looks like I haven't used it at all. I just rinse the brush off really well and then put the cap back on. I use one each cycle and they work great. They are good for the holes too... I can't imagine they would damage the holes in any way because the brush is so soft. If any of you are thinking that you need to go out and buy some, make sure you get the smallest size in whatever brand you find. The "tiny" size in these proxabrushes is perfect for the holes, but much bigger and they wouldn't fit.
If anyone is experiencing the same problems I was, I hope this helps!