Multi-Boxing and Gearswap

I'm having a bit of trouble with Dual boxing and Gearswap, and am hoping someone can point me toward a fix.

The Issue I'm having is the following: 
When I'm using one character and swap to say my PDT set or swap to a hybrid DT/acc set on my RUN while tanking, the keyboard command also takes effect on my dual boxed character's window while not in focus. The reverse is also true - so my BST alt swapping to their pet DD set causes my RUN or BLU or w/e job I'm on on main to also change sets on me, based on the cycle (normal > Acc > Pet Melee on alt, Normal, Acc, PDTTank on my RUN as example). Is there a command I may be missing in my Lua scripts to prevent the commands from going cross-character?

Before asked, my gearswap is branched as follows:

D:\GAMES\FFXI\FFXI WINDOWER\Windower4\addons\GearSwap\data\MAIN

D:\GAMES\FFXI\FFXI WINDOWER\Windower4\addons\GearSwap\data\ALT

And the Name_JOB file goes into each folder as necessary.

I'm having a bit of trouble with Dual boxing and Gearswap, and am hoping someone can point me toward a fix.

 

The Issue I'm having is the following: 
When I'm using one character and swap to say my PDT set or swap to a hybrid DT/acc set on my RUN while tanking, the keyboard command also takes effect on my dual boxed character's window while not in focus. The reverse is also true - so my BST alt swapping to their pet DD set causes my RUN or BLU or w/e job I'm on on main to also change sets on me, based on the cycle (normal > Acc > Pet Melee on alt, Normal, Acc, PDTTank on my RUN as example). Is there a command I may be missing in my Lua scripts to prevent the commands from going cross-character?

Before asked, my gearswap is branched as follows:

D:\GAMES\FFXI\FFXI WINDOWER\Windower4\addons\GearSwap\data\MAIN

D:\GAMES\FFXI\FFXI WINDOWER\Windower4\addons\GearSwap\data\ALT

And the Name_JOB file goes into each folder as necessary.

im not sure about the command sent to both instances issue

but the gearswap issue can be solved in a few ways

try using a folder for each char with

D:\GAMES\FFXI\FFXI WINDOWER\Windower4\addons\GearSwap\data\<charname> folder

and if you want to switch between main and alt for both it can be done but its a little harder to do and would require a more involved gearswap code

for example you would need to build each chars job lua and then switch between two other files based on what you want to use

Yeah, my Folder is divided like that. 
As an example: This is the Data folder and its base divisions:
 

And When I hit my button to swap Larien to Acc mode, Nashu's character is also swapped to Acc mode at the same time, even when her window is not in focus etc. This happens for any mode swaps such as if I want Lar in PDT or MDT set, hitting the key for that also puts Nashu in her PDT/MDT set. I'm trying to figure out how to get it so only the character who is in focus is changed.

Try turning on the Sandbox plugin?

Sandbox plugin is always on by default at start-up. 

Bit late reply, but do you have both setup w/ identical keybinds?  If so, that's probably the issue.