Here's how I do it: Click on the spot in the track you want to be the punch-in point, press F7, that sets the "From" marker. Click on the spot in the track you want to be the punch-out point, press F8, that sets your "Thru" marker. Click on the "Punch" icon. In the resulting pop-up window click the "Enabled" box, then click on the drop-down box and make sure that " Use From/Thru from the main toolbar" is selected. Click ok to close the window. Now, if you click in the track somewhere before the punch-in point and click the "Record" icon, recording will punch in at your "From" point and punch out at your "Thru" point.

As for your flute track, try changing it's channel number to a channel number that is different from the one your piano track is set to, or if no piano track then make sure that it set to something other than "0".

Terry

BIAB/RB 2018 PlusPak. Dell Inspiron23 running Win10, 12GB RAM, 2.5GHz i7, Presonus AudioBox USB interface.