Checked out your string positioning on the pic you posted of your dulcimer and more or less duplicated it on one I had here that I was messing with.............when I fretted the middle/melody strings they tightened up just enough to touch the bass and sure enough threw it off. Looks like it is pushing it up enough to release some of the tension on the bass string or unseating it just a tad in the slot.
'Coyote' John Blosser calls DAA The Mode of The Gods... It was my primary mode for better than 30 years. These days I use Ddd also.
Irene- 
I am LOVING this site. I've played the dulcimer for maybe 30 years....and not only do I learn lots more here, but feel good about my still loving playing in Daa. and with my little stick and pick. As i read all this, can recall doing these things to other dulcimers that have lately come into my hands. wonderful advice....THANKS LOADS.
Check your string positions in the scroll head if that is what you have..............Bass string to first tuner, middle string to second and so forth , avoid crossing them because they will pick up vibrations from the other strings. Since you strum right handed I would go clockwise in this order with scroll head pointing left...........
first melody string to first tuner on bottom of scroll, second melody to top tuner on bottom of scroll, middle string to top tuner on far side, bass string to bottom tuner on far side. use the lowest holes on the tuner pegs that will allow you to keep those strings from making big X's....keep the strings a straight as possible...........some folks will tell you it doesn't matter, but it does.
If you have a dulcimer made by Walter Messick, I would stick with his recommendation on string gauges. I have one of his. I took the extra melody string off because I was splitting them with my finger. Other than that I've not had a problem with intonation. I do use an electronic tuner and tune each open string to either DAA or DAd. As of this moment it's tuned DAd.
If you think you'll be tuning mostly to DAA or CGG, then it makes sense to get melody and middle strings that are all the same gauges. However if you will mostly be tuning in DAd or CGc, then get the set with the middle string slightly heavier than the melody string (since it will be tuned lower than the middle string, not the same).
Wow, there is life here, belatedly.
I re-strung the entire thing. Its scale length is 29". I got a couple sets of strings from a local Guitar Center, specifically dulcimer strings by Martin & Co.; they're 3 @ .012 and 1 @ .022. Having just now looked again at the owner manual that Messick included, he recommends 2 @ .010, 1 @ .012, 1 @ .020w. So I suppose I should get a new set to match that.
I don't think the bridge has moved at all; there is no "give" to it.
Perhaps different, thinner strings will improve matters. I'll see to it next week.
It might help a bit to put on a slightly thinner gauge of strings. Heavy strings will be at higher tension/stiffer and will tend to 'bend' the sound just a bit when fretted down, even if the string is perfectly in tune when played open.
What gauge of strings are you using now and what is your instrument's scale length (from nut to bridge)? Is the action high?
Can you use an electronic tuner to test each string?- make sure the open string is in tune, then test each fretted note on that string, trying to use the same light pressure to fret it. If all strings are sharp or flat on the same frets, then the fret placement may be off. If however there is one or more strings that are perfectly in tune on every fret, then it points to a string issue that likely can be lessened by changing string gauge or playing action.
Ken's right--an "intonation situation" (sounds like a new song title!) could also include something like bridge movement, which would knock your intonation out of kilter. If it was fine before you restrung your dulcimer, then you did something to change it. Even small changes in the bridge placement can make a real difference.
When you re-strung the dulcimer, did you take all the strings off at the same time and then replace them all? Or did you remove/replace one string at a time? It's possible that the bridge has been slightly misplaced, and that is what's causing the intonation problem.
Sounds like an intonation situation to me. There are various types of intonation--you can do searches on them (just intonation, equal intonation...)
When I tune my instruments, I first use an electric tuner and then double check them by playing a D on the A string and an A on the D string, tweaking the pegs a bit til I get a sound I like. It sounds like this is what you're doing, too. When I can't seem to make this work with a particular instrument, it's usually because the intonation of that particular instrument is different from what I was expecting. You'll probably find you have a preference for one type over another--which is a really good thing to know when you're getting your next dulcimer!
I've recently re-strung my dulcimer. I keep it tuned DAA for now, but I have an oddity in tuning.
After bass is tuned to a pitch pipe's D, I do the typical relative tuning of the A strings using bass 4th fret. This sounds fine. Also, if I walk a scale up from open to 7th fret, I get a normal D or A scale on the respective strings.
But when I hold 3rd fret on the melody pair and strum, the result is a significant dissonance in the bass. The 3 upper strings sound fine together, but the bass is off.
For the moment, I've gone to tuning the other way, tuning bass to A 3rd fret. So this sounds fine, but of course now it's off elsewhere.
As a mathematician, knowing that I can get a correct scale on all strings individually (so the frets are of course properly placed) but I can't tune one to another and expect to get a matching chord elsewhere on the fretboard is a deep weirdness to me. I mean, this is about sonic frequency, and all things being equal -- frets placed right, relative tune from one to another -- these ought to be Right.
Can anyone offer an explanation for why I get this discordance?
