At the risk of hijacking Brian’s original query about both E notes being sharp, I want to pursue the issue of the discrepancy between the two Es, as this is a typical problem with many D chanters. Sorry Brian 
Seagull, see Pat Sky’s comments if you have not already. It is a common problem with D chanters. You discovered one way folks deal with it…
I have to do a “tinkers E” as someone put it. Basically its just lifting only the ring finger of my right hand off and lifting the chanter off my leg.
Actually, the fingering you describe is a way to play harsh or hard E, just give it a little more pressure. It is not completely in tune on my D chanter, but the hard Es are wonderfully in tune on the C chanter that I made recently, and have a really nice tone - a really wonderful way to color the E note, so you might find it useful to aquire the dexterity to use that fingering.
You might find that the pitch of the second octave E is sensitive to bag pressure and some folks manage to reign it in by better pressure control and the standard fingering, blowing it into tune as it were. I think that beginners tend to over-pressurize the second octave, anticipating difficulty in reaching and maintaining the note. I know I had this problem in spades, at least. So things might improve as you get more relaxed.
The problem lies in the fact that the first note above the bottom note of most woodwinds has problems. The E is the worst note on the flute both in pitch and tone. What will actually correct the problem is to extend the length of the chanter on the bottom.
Pat,
Very interesting. This must be why flutes have a lower foot joint?
I’m wondering if the opposite is true, if having a bunch of crap stuffed into the bell to bring on the hard D and keep it from gurgling has the opposite effect of extending the bell - might this be a source of discrepency in pitch between the lower and upper E notes? It seems that most folks D chanters I have looked at need some degree of ‘inducement’ in the way of debris stuffed into the bell in order to play the hard tonic note. I wonder if differences from person to person in the amount and position of their rush material could be a factor in the variablity of the E tuning?
Still, I think that there must be some contribution to the E discrepency that is not due to the chanter design, since there are plenty of examples of people playing a particular make of chanter who do not have this issue and some who do - same chanter design different reed. Although some folks may just be better at blowing the E into tune.
As my reed making improves, this probelm with the Es has vastly improved, so has the ability to get the hard tonic D without the need to ‘rush’ the bell, so simulatneously out came the packing in the bottom of the chanter, so I guess I need to put it back in and see if the difference in pitch of the Es increases.
Ahghh! too much for me to consider without the aid of a pint of beer,
Best regards,
John.