Hello - i posted this to the other discussion on trouble notes. This may help as well.
Try experimenting with the fingers on the right hand as you don`t need them all for all occasions. I use just my left hand fingers (ie no right hand fingers) when i want an Eb that is slightly flatter and a little duller (for an Eb in a C minor chord) . I add my little finger and the one next to it on my right hand is i want a brighter and sharper Eb (such as a D sharp in a B major chord)
middle Eb can be helped with a combination of different fingerings. I regularly use three depending on the context of what you`re playing and how you approach the note ie. If it`s very quick finger work, then i use the basic Eb fingering. If it`s an Eb in a quiet passage then i have another and if i need an Eb that is slightly sharper or flatter i`ve got fingerings for those two as well. it`s basically a different combination of right hand fingers - try adding and taking away different fingers on the right hand with your normal Eb fingering and hear what difference it makes.
Have a look at :
http://www.wfg.woodwind.org/bassoon/
which has a few alternatives
or:
http://www.people.vcu.edu/%7Ebhammel/main/bassoon/fingers/chart.html#
or another one in even more detail :
http://www.idrs.org/BSNFING/FINGHOME.HTM