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Try a PS/2 mouse?
Try to remove/disable one of the audio cards to see if there is any connection?

Moved.

Although it's loaded in via legacy, it still needs to go via the USB controller and I'd imagine invoking the USB drivers. USB was never a DOS era thing so there's bound to be hiccups. I'd agree with dr_st and go for a ps/2 mouse.

dr_st wrote:

Try a PS/2 mouse?
Try to remove/disable one of the audio cards to see if there is any connection?

Ok so I took both cards out of the machine. The mouse still causes stutters in the actual animation in the games I’ve tried. For example Guybrush pauses his walking in MI1 if I move the mouse. Releasing the mouse causes his walking to animate normally.

I’ve purchased both a PS/2 and plain old serial mouse off of EBay. When they arrive I’ll try those and see how it goes. I’ll report back what I find. Thanks!

try another driver?

Download the DOS NSSI program http://www.navsoft.cz/products.htm get the latest build and unzip it to you dos partition.
Load DOS with a clean boot (nothing, not even himem.sys) and load ctmouse. Run NSSI and select the benchmark from the menu (either one). Look the your real time benchmark result and then start moving the mouse in a continuous circle. If your score drops a lot (25%+ ) it's a problem with the mouse driver.

Is the USB controller using the same IRQ as the video card? That would be my guess.

I am also guessing that the USB controller IRQ is hard linked to the same slot that the video card is in so no matter what, you will probably get that video stuttering when using a USB mouse in DOS.

Is there a PCI latency adjustment in the BIOS of that board? If so, try reducing it to 128 or 64.

See here for some options that should let you adjust it even if there isn't a setting in BIOS. TweakBIOS is what I used to use back in the day.
http://www.mdgx.com/speed.htm

First I want to thank everyone for all of their help and their willingness to offer ideas. I ended up buying a generic PS/2 optical mouse:

https://rover.ebay.com/rover/0/0/0?mpre=https … %2F302835643311

It completely fixed all the issues. I can move the mouse as much as I want and it no longer affects the audio or the animations. I am so happy this fixed it. I can’t believe how unusual of an issue I had on my hands.

Again, I thank all of you for helping me solve this issue!

Yep, having a mouse controller instead of interrupting the CPU every time the mouse send back a bit of data can do that 😉

doaks80 wrote:

Yep, having a mouse controller instead of interrupting the CPU every time the mouse send back a bit of data can do that 😉

This makes me wonder, could we/someone make a new type of mouse controller card ?
One that's more intelligent (with it's own processor), causing interrupts fewer time or uses Memory Mapped I/O instead of I/O ports ?
The current siutation isn't exactly ideal. Serial Mice work fine, but cause much CPU load, whereas PS/2 style mice are rather jerky in Windows 3.x..

Jo22 wrote:

This makes me wonder, could we/someone make a new type of mouse controller card ? One that's more intelligent (with it's own pro […]
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doaks80 wrote:

Yep, having a mouse controller instead of interrupting the CPU every time the mouse send back a bit of data can do that 😉

This makes me wonder, could we/someone make a new type of mouse controller card ?
One that's more intelligent (with it's own processor), causing interrupts fewer time or uses Memory Mapped I/O instead of I/O ports ?
The current siutation isn't exactly ideal. Serial Mice work fine, but cause much CPU load, whereas PS/2 style mice are rather jerky in Windows 3.x..

Well of all the hobby expansion card projects you could do, this is probably the most feasible. You would probably want to start by looking at bus mouse controller cards which are an extremely simple design and were made for the win3.1 era.