Do check the breath pressure being applied - obviously not enough support can fail to raise the pitch, but with some soft reeds, the E can actually be forced down by too-intense breath pressure - this is usually the situation where adding RH3 lifts the pitch back up.
A small clip across the tip of the reed of around 2mm (I always use "end-cutters") may correct the profile enough to solve the flatness. I believe this is due to the "new" tip being slightly thicker rather than the reed being shorter thus sharper.
The 3rd finger is a good strategy for a quick fix (say in ensemble playing, assessments etc), but do keep returning to the regular "short" fingering in lessons rather than have it become a permanent fix.
With inexperienced players, try to avoid conductors telling them they are "too loud" - it may result in clamping down on the reed and being too sharp - or blowing too softly and not reaching supported pitch. Generally speaking "too loud" in a beginner means "out of tune" - a generously supported dynamic is actually welcome if in tune - so focus on pitch rather than volume.
Good luck. Neville
Christchurch New Zealand
Bassoonist / Teacher / Conductor