NEED HELP haaving trouble converting Blu-Ray 3D to VR capable file

[Hoover1979]

I am having some real trouble here.

I start by format shifting my Blu-Ray 3D disc to an MVC3D MKV file with MakeMKV.
Then I convert it to 3D SBS with BD3D2MK3D (the only program that allows me to make 3840x1080 as others limit me to 1920x540)
but when I run them in ANY VR media player they are squashed down ruining the aspect.

Yesterday I was able to use Handbrake to convert them to the same size with DTS passthrough to preserve the audio (I have 5.1 sound) and they played perfectly.

However, as of today Handbrake is not playing ball refusing to let me set any width higher than 1920. This means I would have to convert to 1920x540 and lose a ton of detail or convert to 1920x1080 and have the aspect squashed the other way, ruining the video. I can't do anything with Format Factory as it never gets past "waiting" and never starts to encode (and that program doesn't support DTS).

Is there any way to get Handbrake to act like it was yesterday and let me convert from 3840x1080 to 3840x1080? It's the only way I can get my 3D movies to run in VR at the correct aspect.

Please Assist.

[netmask56]

I don't have Handbrake but I do have Vidcoder which is built on the Handbrake engine. In settings no problem setting 3840 x 1080

[Hoover1979]

I don't have Handbrake but I do have Vidcoder which is built on the Handbrake engine. In settings no problem setting 3840 x 1080

Thanks for your help. I bought Whirligig VR player and it's the only VR player that plays my SBS 3D videos at the proper aspect. It also used direct show so I can use Smooth Video Player. Best $6.00.00AUD I spent in a long time.