Observing negative peaks after cleaning GPC column

[labgurl23]

Cleaned GPC column with 50% acetonitrile, 50% MEOH, for 5 min in the reverse direction, and then an hour with the normal direction. But when I ran my samples, the peaks looked really weird.
Also, when running the samples, I stopped the run in between to add a sample. Is it possible that this could have affected the machine or introduced pressure issues?

[tom jupille]

Lots more information needed:

• what type of column (silica. PS/DVB, . . . ?)
  what type of detector (RI, UV, ELSD, . . . ?)
  by "weird" are you referring to them being negative or is their another issue?
  do all the peaks show the same problem?
  did the problem only appear after you restarted or was it there from the beginning of the run?