I have the same issue.
One minute I'me recording a track all ok, then just try to do another take and input levels are blank, just peaks, though I can hear the audio. Try to record and no audio recorded in the clip.
Restarting S1, no difference. Reset audio interface, restart PC. Still no go.
Open another song, then it's fine. Re-open last project, it is fine.
Next day, the same thing again!
I never had this issue with any (since v2.4) of prior versions of S1
So, yes. I have the same issue and it is annoying, specially when a client is waiting for me to sort it out.