If you had air in it the first time and did not bleed it properly like the factory manual shows, you could possibly have some premature wear/damage to a piston and cylinder/motor/pump block from it not being bled all the way the first time.
It will operate when it is cold, but after it heats up, it will slow down and if that is the problem, you may have some damage there.
It is so critical to bleed them properly the first time before you start the engine and engage the drive, or you can have some serious damage in a hurry.
From just tipping the machine over when working on it if the fluid was drained, it could be air bound. You have to bleed them like the manual tells you to first depending on how far you took things apart.
If you only worked on the right side gear box and didn't drain anything from the hydro unit, you might just have a little air in it that is bubbling.
Switch the release lever to the released/dis-engaged position and try running it forward and reverse, then re-engage it, sometimes that helps, but if you drained the oil out of the hydro system, you have to bench bleed it first before you put it back in the chassis and follow all the steps in the manual. Make sure you use the correct oil also.