Problems with 2.2.5

[Star destroyer 18]

I recently downloaded 2.2.5, followed all the steps in the included text document, but ended up with a "unique" mash of vanilla FOC and 2.2.
Examples:
-All ships use the same layer in space
-Wedge and wraith squadron grant Salvage bonuses on imperial space forces destroyed during Hunt for Zsinj GC
-Ships travelling between planets do not stick to the hyperspace lanes just like vanilla
-Hardpoints are the old vanilla design, not the new reduced in size designs from 2.2
-AT ATs and T2Bs fire "continuous" bursts of lasers at targets, intended?
Changes implemented observed like Empress is 20,000 instead of 10,000 and Validusia being used by the Empire. The game feels and looks fine other than these points like the UI, boarding shuttles, etc
Did I install it wrongly?

[Corey]

You likely have files in your base game data folder overriding mod files.

[Star destroyer 18]

Then how do I resolve it?

[Star destroyer 18]

Just downloaded 2.2.5, now I can't play at all as I get Exception! See..... when I clicked on the bat file, though I did the same steps as previous installations with the demo and 2.2, please help.