The "Always Use MP4" preference isn't respected for all files in a batch run.
To reproduce
Resulting files will all be M4V except for the 1st file which will properly be MP4.
HandBrake 1.3.0
Windows 10 1909
Preferences

Resulting Queue

Guessing you mean M4V instead of MKV. 馃樃
Thanks for the report, we're looking into it.
Guessing you mean M4V instead of MKV. 馃樃
Thanks for the report, we're looking into it.
Yes I do, just fixed :)
FYI, single files are also affected. I'm using the 1.3.0 on Win 10 1909, too.
Drag / drop a file onto HB and it assigns .m4v output extension, despite the output preference as .mp4.
Does the fix resolve both issues??
All The same issue.
Now resolved. Thanks for the report.
Will be part of 1.3.1 (New development nightly snapshot build will be available in the next day or so)