Pretty sure its been reported, I didn't find it searching though.

I haven't put my finger on what the exact cause is but recently I have noticed that I only get email check-in online notices for some flights. I thought it was related to multi-segment flights but last week I flew one and it worked without an issue with all email notices being received.

Any ways, two weeks ago I flew CLE-EWR-LIS return CPH-EWR-CLE and no online checkin notices.

Last week I flew CLE-BOS, BOS-EWR-RIC, RIC-CLE and received email notices for checkin.

This week CLE-LGA, EWR-TPA, TPA-CLE and no email notices for checkin.

FWIW, only this weeks flight had any modifications done to it after purchasing at CO.COM.