You left Pikatimer exactly as it was before? You have your usual calibrated seconds and you kept 50 as your wanted seconds? You didn't adjust your delays beforehand? It was the same exact delays as before?
If you left those alone and you hit 48 seconds again, then move the DS clock to two more minutes later. Do not adjust your delays until you have tested that you land on the right seconds. Adjust your DS clock only until you consistently get the right seconds. Then you can start adjusting your delays again.
If you discover afterward that your seconds change due to a delay adjustment, then test this again by doing the RNG once more to see if it was a random jump to the wrong seconds. If not, then adjust your DS minutes again, without adjusting your delays, until you're on the right seconds again.
Yeah, I didn't touch anything. I'm just going to change my IV spread since I can't seem to hit that one.