I had this happening with a shitty PC USB interface. The interface kept sending some sort of message and that DOES clog up the MIDI port.
You need to filter your MIDI signal and give the C64 only what it needs. Disable aftertouch, polyphonic aftertouch, SysEx messages, even program change if you are not going to use it. Only allow the CC data that will actually work with the C64 and nothing else.
Try other MIDI emulation modes instead of Datel, for example SIDWizard uses NameSoft. In the case of Station64, that works pretty much with anything as long as you reconfigure it, so no need to stick to Datel emulation if it's unoptimal.
Also re: Station64, make sure you have the latest version, I have helped the writer fix some of these problems. It still happens but only when you send a LOT of notes REALLY fast, which is not very normal. Nowadays it works quite well, but sending notes AND changing parameters in real time can all produce lags and notes "swallowed" by the system if it is all too much for the C64 to handle.
Last edited by akira^8GB (Oct 9, 2015 5:55 pm)