If you capture as 32k, you should be able to capture all 4 channels at once, though you may have to customize the capture preset.
editing 32k in a 48k timeline may be the cause of your sync problem, so I'd recommend converting the 32k audio to 48k using batch export.
I'd try this method first, and if that doesn't work, then try capturing as 48, which will only allow you to capture 2 channels at a time. However, duplicating the offline clip and capturing a second audio-only version of it should be fairly simple if you need whatever iis on channels 3&4.