All PRED=0 after removing IIV

Hello, I am using an existing model to describe new study data. The covariate model needs to be updated. The model is quite complicated: time-varying PK and many IIVs. It takes a long time to converge. I want to remove some of the IIVs to shorten the run time for covariate search. Unexpectedly, after removing the IIV (one at a time), PRED=0 for all records. I got the same issue for multiple IIVs. It's a proportional residual model on the original scale, IPRED was fine, so dose was given. The model converged and parameter estimates were close to values before removal, so it didn't seem like an estimation issue. Before removal, PRED was fine and not a small number, so it couldn't be a digit issue (I also tried to change format for $Table but it did not work). I am having a hard time understanding why. Apology that I cannot post the full control stream here. It's NONMEM 7.5 and intel fortran. Hope you can point me to the right direction. Really appreciate your guidance! Thank you, Dongfen