Is your IQ250 firmware up to date?
El Capitan made a few changes to USB3 communication protocols and some of the CCD backs will need a firmware update for full compatibility. But my understanding was this should not effect CMOS backs that are using current firmware. Have you spoken with your dealer?
8.3.4 with support for El Capitan was released by Phase One about four weeks after El Capitan's release. That dealt with most of the bugs/quirks that the new OS imposed on C1.
In general we strongly discourage professional users from jumping to a new OS for a few months. This is even more important to head if your living depends on tethering; nearly EVERY OS release breaks tethering for at least one of the cameras that Capture One supports. There is very very little upside to updating your OS immediately (some minor new features that aren't core to pro workflows) and a decent chance of issues with at least one of your core software or hardware pieces or the operating system itself. See our warning when
8.3.4 shipped.
You're always welcome to call us or email me about current C1+OS suggestions. Sounds like this could have saved you a headache!