Besides the issue that Catalin already mentioned with the # of turns in the build queue having disappeared, another thing that disappeared was the Status of Agents that are En Route or assigned to a minor's homesystem (shows blank for anything but Awaiting Assignment at xxx and En Route to xxx when being repatriated [war declaration]).

Also, when you establish a trade route, the income display doesn't automatically update. You have to click somewhere else, and then click back on your system. If you then change the route's destination to another system, the previous value is not updated to zero, it keeps the previous value.

When you Retire and start a new game, the Diplomacy icons keep their previous (first game) settings, they're not refreshed - the icon colors (they're great BTW) remain, and the tooltip Played by Player is shown in the faction of that first game (playing the Romulans, retiring, and starting a game with the Dominion will show Played by Player in the Romulans icon).
Also, the icon for the player's empire should probably be grayed out.

In the Assault System screen, the tooltips for the Hull bars of ships (and OBs) read Hit Points, same as for Production Facilities; since the Shield bars read Shield Strength, the Hull bars could read Hull Strength. A detail, really. PFs could read Structure or something, it'd sound nicer IMO.

When assaulting a system, if you Stand Down you get the Defeat status. It should be Stalemate?

When you subjugate a system, you don't get a SitRep message in the Turn Summary.

The exception when you start a game in a small map and then retire and start another one in a tiny map now produces a lot more index out of bounds warnings, a gazillion of them.

In the Embassy screen, the Turns display for all minors always displays the current turn number, regardless of when the minor was contacted.

When setting up a Payment exchange, if you click on the bars to set an amount, you then cannot set it back to zero - seems to have a minimum of 250 (max is 5000, probably related to the default amount of starting cash). Happens for both Immediate and Recurring.

If you have one Orbital Battery I already built and give the order to upgrade it to OB_II, you can can still queue more OB_Is after the upgrade order, which you shouldn't. If they're bult in the same turn, the upgrade has no effect (though it costs Raw Materials), both OBs will be OB_Is.

Also, while the time to build the upgrade is correct (half the Build Cost, consistent with other upgrades), the Raw Materials cost I'm not sure. It's also half the RM cost of the upgraded version, instead of the difference of costs. Is that intended? Right now the RM costs for the 3 versions are 40, 50 and 60, which means each OB_I that is upgraded to OB_II costs 25 RMs instead of 10.

BTW, there's a problem with the Romulan's Night Patrol which I have already fixed. I've also fixed the RefireRate display issue.
And I've set the Dominion to only be able to colonize Rogue planets. I'll see if I can change the base race to the Founders.

Hi everyone, i'm back!!! I noticed the empire intelligence structures are disabled in this new build!!

Hey, welcome back.
Yes, we're replacing Intel production with a Personnel-based system. It's still a WiP though, it'll take time to fully implement it.

BTW, some of these issues have already been fixed in the 20130203 build.