1) After creating a project and Quiting and then Opening it again, most but not all media is offline.

Opening the Media Brower and highlighting all clips and clicking LINK -- all missing media reappears.

The Sequence icons are blank unless I Refresh them.

2) Selecting a clip and hitting the Motion Effect button brings up a control box but nothing can be entered. (Once it reported 80%.)

3) The FORWARD and REWIND butten *should* move to next edit >>>> but *not* enter Trim mode. But, it does enter Trim mode which only should occur with PREVIOUS EDIT and NEXT EDIT.

4) The DNxHD export has 44.1kHz audio not 48kHz.

FWIW, if memory serves me number 3 happend on Media Composer as well. The default FF/REW hotkeys always entered trim mode after jumping to an edit. Always thought that was a bit strange. :-)

Are you on Mac or PC? Which OS version number?

In 1) were the original linked or imported?

In 3) is there anything  different checked inSettings / Composer / FF / REW tab?