Glad it's not just me!
My explanation for why I feel this way is that I always feel a sense of personal accomplishment when I have managed to sock away another $1,000 in my savings account. Seeing the first digit of the balance be one number higher than it was in the preceding months validates for me all the hard work I've done to be able to put away a few hundred here and there. To then take out more than $1,000, even for a very good reason/purchase, feels like defeat. I know it's dumb, but I can't help but think, "Well, that's gone," even when realistically, it's not usually "gone," it's just been applied toward something.
During the fall, for example, we spent $1200 on repairing and shoring up our roof before we had solar panels installed. We had the money set aside for it, I knew the roofer was giving me a fair price and would do good work (he did; he even went above and beyond), I knew it was a wise decision, etc. Just like you, I had analyzed it to death and knew it was a sensible expenditure. But still, it pained me to write the check and see our balance drop.