Batch file stops running after the first command

Add call in front of the commands you’re running.

You can also change this to a for loop, so:

FOR /L %%i in (1,1,5) DO CALL HTMLMATCH.EXE D:\Raj\compare%%i%%\a%%i%%.html D:\Raj\compare%%i%%\a%%i%%.html D:\Raj\compare_res\a%%i%%.html