Andrus Lauringson 

Untested (AI Solution) but...

ControlSetChecked "&Match case", 1, "Find and Replace"
ControlSetChecked "M&atch whole word", 1, "Find and Replace"
ControlSetChecked "&Target", 1, "Find and Replace"

In AutoHotkey v2.0, ControlSetChecked expects the control identifier first, then the checked state value, then the window title.  By putting 1 first and the control name second, AutoHotkey is interpreting the control name as a non-numeric checked value, which causes it to toggle instead of explicitly setting the state.

Thanks, but according to Autohotkey 2.0 documentation, the command syntax is:
ControlSetChecked NewSetting, Control , WinTitle

Changing the order results in an error message.

Andrus Lauringson 

Just goes to show AI isn't right for everything!!  Maybe something in this will be helpful?

Given that your syntax is correct, the issue is likely that ControlSetChecked with value 1 is somehow toggling rather than explicitly setting the checkbox state. This could happen if:

1. The control isn't being properly identified - The "&Match case" text might not be consistently recognized
2. Trados Studio has custom checkbox behavior - Some applications implement non-standard checkbox controls

Here are better solutions:

Solution 1: Check the current state first

WinActivate "Trados Studio - "
WinWaitActive "Trados Studio - ", , 4
Send("^f")
WinWaitActive "Find and Replace", , 4

; Only check if currently unchecked
if !ControlGetChecked("&Match case", "Find and Replace")
    ControlSetChecked(1, "&Match case", "Find and Replace")

if !ControlGetChecked("M&atch whole word", "Find and Replace")
    ControlSetChecked(1, "M&atch whole word", "Find and Replace")

if !ControlGetChecked("&Target", "Find and Replace")
    ControlSetChecked(1, "&Target", "Find and Replace")

Solution 2: Use ClassNN identifiers instead Use Window Spy to get the actual ClassNN of each checkbox (like Button1, Button2, etc.):

ControlSetChecked 1, "Button1", "Find and Replace"  ; Replace with actual ClassNN
ControlSetChecked 1, "Button2", "Find and Replace"
ControlSetChecked 1, "Button3", "Find and Replace"

Solution 3: Force uncheck then check

; Force uncheck first
ControlSetChecked 0, "&Match case", "Find and Replace"
ControlSetChecked 0, "M&atch whole word", "Find and Replace"
ControlSetChecked 0, "&Target", "Find and Replace"
Sleep(50)
; Then check
ControlSetChecked 1, "&Match case", "Find and Replace"
ControlSetChecked 1, "M&atch whole word", "Find and Replace"
ControlSetChecked 1, "&Target", "Find and Replace"

The most reliable approach is probably Solution 1 or getting the proper ClassNN identifiers with Window Spy for Solution 2.

None of these solutions worked, it's still a toggle.
With solution 3, due to Sleep(50) it was visible how on first use, the script added the checkmarks, and on the second use removed them.