I had issues with my CR Touch and the Ender 3 Pro board/firmware. Seemed to never work correctly. Finally got tired of it and put a bigtreetech v3 with display combo. Still had issues with bigtree's firmware. Went to TH3D and grabbed their firmware and compiled my own. Works much better now. Babystepping can be key while printing. Also I found if you leave the stock springs and adjusters on, i still needed to manually level my bed every once in a while before running a ABL.
I would start with compiling your own on the stock board. If that doesn't help then maybe go with a better board. Mine is a lot quieter now. It's the one I travel with for work, so sometimes it's running in a hotel room with me at night.
I will say that with the stock board and CR Touch after it homes when you are trying to set the Z offset it lifts like 10mm above the bed. Took me a long time to understand how to get the offset correct. My CR10 with ABL would lift just a few mm after homing when setting Z offset. Other things are after homing, the mesh may be deleted so you have to rerun your ABL. Another issue I have heard is that fade height being set to anything other than 0 when running ABL may cause issues also.
Having a single Z motor can cause issues. The gantry can sag when the head gets to the right side, especially if you have direct extruder setup. Make sure all wheels that have the concentric nuts are adjusted properly.
Sometimes using a terminal like pronterface helps too. If you run a M503 it should give you the mesh. This is key. You can scroll up to see the mesh change.
Another issue I have seen with mine with the stock board is running G29 multiple times in a row. It seemed to mesh using the numbers from the previous G29, which added height. I could never confirm this properly or find anything in searches that this happens. I know it sounds weird but I would see my numbers go up in pronterface and my first layers would be horrible.
I have been struggling with my Ender 3 pro for almost a year. Great little machines stock but once you start upgrading it you start running into little issues that are frustrating IMHO. My CR10 and D3 Hero are to a point where I can start a print and walk away. My CR10 is a shadow of its original form but it is bullet proof.
Here is the board I am currently using in my 3 Pro:
BIGTREETECH SKR Mini E3 V3.0 Control Board + TFT35 E3 V3.0.1
Aurora Tech, Chris's basement and Teaching tech are my 3 go to on YouTube.
Below is the upgrade of the v3 board. Watch out for the pins for whatever sensor you are using. I had to do a little research and split the connector to get rid of the Z limit switch. Also it helps to get bootlace ferrules and JST connectors from Amazon.
https://youtu.be/dtwWnz2-5VQI hope this helps