Yes, the R2400 is a fickle beast. I'm not sure whether it's that particular model of printer, or the IJM carts, which are a much older design that the one currently used in refillable carts for other desktop printers. IJM went through a couple of iterations with R2400 carts, and the final one (AFAIK) required vacuum filling from the bottom, which was very tedious.
In my view the gaps I assume you are seeing in nozzle checks are unlikely to be clogs (unless you're living in a desert with 0% humidity). And especially if they occur in different nozzles. Rather they're most likely to be air that has got into the system. The question is, how did it get in there? Unfortunately that question usually is very hard to answer. There are quite a few people who eventually gave up on the R2400 for that reason. Best of luck.