what you described as perfectly comfortable on your other bike was 'flat handelbars higher than saddle'
then you switched to 'bullhorns with deep drop lower than saddle'

can't you see how this would effect your position on the bike and saddle ?

for a baseline why not set up your new bike identically to the old ?
make the saddle height (the actual distance from pedal spindle to saddle top) the same
make the bar height the same (if you are uncomfortable only when in the drops then maybe the bars need to be even higher)
make the reach the same (the distance from the saddle to the bars)

i cannot see how a perfectly comfortable saddle set up the same way could become suddenly uncomfortable...