[Shamus]

Are you using 1.0.7? The extension problem was fixed in the latest version. I'm not sure about the command line (as I hardly ever use it anymore), but I'm pretty sure it works the way it should (again, in the latest version). You can immediately tell what version you're using by running it with the GUI and going to Info|About.

Here's the latest VJ run from the command line on my system:

Microsoft(R) Windows 98
   (C)Copyright Microsoft Corp 1981-1999.

C:\MinGW\Source\virtualjaguar>vj -help

C:\MinGW\Source\virtualjaguar>type stdout.txt
Virtual Jaguar GCC/SDL Portable Jaguar Emulator v1.0.7
Based upon Virtual Jaguar core v1.0.0 by David Raingeard.
Written by Niels Wagenaar (Linux/WIN32), Carwin Jones (BeOS),
James L. Hammons (WIN32) and Adam Green (MacOS)
Contact: http://sdlemu.ngemu.com/ | sdlemu@ngemu.com
Usage:

vj [romfile] [switches]
  -? or -help     : Display usage and switches
  -frameskip 1-10 : Enable frameskip 1 - 10 (default: none)
  -joystick       : Enable joystick/gamepad
  -joyport 0-3    : Select desired joystick port
  -bios           : Boot cart using Jaguar BIOS ROM
  -nobios         : Boot cart without using Jaguar BIOS ROM
  -dsp            : Force VJ to use the DSP
  -nodsp          : Force VJ to run without the DSP
  -pipeline       : Use the DSP pipelined core
  -nopipeline     : Use the DSP non-pipelined core
  -gl             : Use OpenGL rendering
  -nogl           : Use old non-OpenGL rendering
  -fullscreen     : Enable fullscreen mode (default: windowed)
  -window         : Enable windowed mode
  -pal            : Force VJ to PAL mode (default: NTSC)
  -ntsc           : Force VJ to NTSC mode

Invoking Virtual Jagaur with no ROM file will cause it to boot up
with the VJ GUI.

My guess is that you're not using the latest version...