I found autorun bug in nightly build (maybe also earlier) 2.4.6-x86-r28017.
I tried to use to LOAD and then execute ML program (single file, no diskimage) with command e.g.:
x64 -autoload "test.prg" -keybuf "sys49152\x0d"
ML program is written for testing VIC-II exchange border color.
x64 starts, executes SYS and it works not - like there's not loaded anything. But then I executed program directly in x64 (without restart) and works. I meant that problem is in delay.
So, I added -autostart-delay 10 to command line and it does the same.
The same effect has x64sc, xscpu64 and xvic (xvic has other test program).
In case of xvic is also problem with autorun Basic programs - crashes.
Only in case x128 this works without problem.
Please look at this bug. I wrote VB app for using it with every file - reads first 2 bytes of PRG and creates keybuf. It was working in VICE 2.4, later were changed options to use keybuf, so I needed rebuild it and today I was working, but really don't know reason why it works not.