E.g. if you go to upgrade a science officer's "Tachyon Harmonic I" skill, and click the icon to get the "Skill Details" display, and look at the stats, then click the "^" arrow under the "Tachyon Harmonic I" box, the resulting "upgrade" stats //always// look worse.

E.g. for THI / 1, it said "50% chance: Knocks Back +5.6 feet, -25 Target Shields",
but for TH1 / 2 it said "50% chance: Knocks Back +5 feet, -23 Target Shields"

Since I figured this has to be a display bug, I upgraded. And now it says "50% chance: Knocks Back +5 feet, -25 Target Shields".

All the other stats similarly offered to generally get worse for me, but all now show the exact same values as THI/1.

WTF? =)

There's a graphical glitch when upgrading skills that makes it show the tooltip for the rank before current instead of the next. This confused me quite a bit too at first, since I went to level up high yield torps on my first character and going up in rank took it from 1 minute cooldown to one minute five seconds. I thought this was odd, and found out that if you click inside the skillbox itself (in the box above the up/down arrows, not the tooltip) it will update the tooltip to the stats for the rank you have selected to level up.

I'm assuming this is the issue you're having, where when ranking up the tooltip shows data from a lower rank than you actually leveled up to.