In relation to this comment.

I finally got to the bottom of this - the $T fix was NOT the issue.

The carets escaping the percent signs must be shown in the doskey macros list, then all works fine:

D:\pe\home>doskey /macros
cd=cd $* $T call title ^%cd^%

In Windows without clink, both:

D:\pe\home>doskey cd=cd $* $T call title ^^%cd^^%

and

D:\pe\home>doskey cd=cd $* $T call title ^%cd^%

function the same but, with clink, only the first one changes the title to match the cwd. The second one always displays the cwd that you just changed FROM.

My workaround is just to double the carets but I guess that's a bit of a bug in clink's doskey implementation?