Also going to note that, based on training mode, SFIV doesn't seem to handle keyboard input ENTIRELY correctly if you're hitting buttons fast. And I'm not just saying this because I suck at the game. I'm saying this because I got C. Viper to launch a kick-based special move by hitting punch.
Were you mashing? If so, that would explain it as certain attacks have priority over other attacks. That's how plinking exists.
So with keyboards, fighting games in general seem to get confused by how keypress/keyreleases are sent. Half-circles generally don't work right unless you're really deliberate about the keypresses, although SF4 also parses db, fb as a half circle so no issue there.
What I was physically pressing on the keyboard was, in sequence,
Which for c. viper should just be a crouching kick followed by some shoryuken thing.
Except it was taking the heavy punch as another kick and doing a different combo.
I THINK what was happening is that I released the first light kick button too late, and in doing so it... somehow sent another kick input to the game instead of what I was actually pressing. So it either ignored the punch entirely, or the punch and a second kick were both sent and the plinking thing you described happened.
This also might be, strictly, and issue with my laptop's keyboard.
--- edit ---
Oh wait just saw a video on plinking. It does that with almost any simultaneous button press for me :(