Unless changed in later models, the aforementioned "adjustments" on the HWH hydralic arms change the slide at closure [might allow you to align the paint strips on the outside of the coach--for example]. As mentioned, you should allow the HWH to run an extra second after closure to load the cylinders to keep the slide closed during transit. If this doesnt result in total closure at the top, the slide may have gotten slightly out of position and is binding against the frame--usually a few miles of driving sorts all this out.
However, if the the slide is hitting the top of the frame or side, you can, as suggested, run the slide full out and back to equalize the cylinders. "Adjusting" the cylinder arms usually isnt needed--the cylinder arm length is set at the factory to accommodate the travel of the cylinders. Once set, the overall travel length should cover any minor changes in slide position.
The adjustment at the end of the arm [large set screw and locking nut] can be used to raise the final height of the slide in the closed postion, but more often than not, the slide has settled a bit over time and needs to be raised slightly.
Think I would veryify that the slide is clearing the coach wall frame on all 4 corners before doing any adjusting.....keep us posted.
2003 40' MDTS
Garden Ridge, Texas