Skquery gui formatting sucks. You should consider using TuSKe or normal SK for that. I have experimented with this before and it never updates the command. It keeps the same one for all of them.

I have never used TuSKe before so I am going to show you can example of how you can do it with normal SK and Skellet.

Code (Skript):

1.  
2. command /chest:
3.     trigger:
4.         open chest with 3 rows named "test" to the player
5.         loop 20 times:
6.             set slot loop-value - 1 of player's current inventory to 1 of white stained glass pane named "%loop-value%. location"
7.  
8. on inventory click:
9.     set {_i} to clicked slot
10.     if clicked inventory is player's current inventory:
11.         name of player's current inventory is "test"
12.         cancel event
13.         make player execute command "checkval %{_i}+1%" #made it +1 because in the formatting you put -1...
14.         close player's inventory
15.  
16. command /checkval <integer>:
17.     trigger:
18.         message "%arg 1%"
19.  

If anyone has an example of a TuSKe gui doing this, feel free to send an example.