Problem with geneScore function in SeqGSEA

[mightywurlitzer]

Hello -- I'm using the SeqGSEA 3.0 R package to analyze RNASeq counts generated with htseq. I did some processing about 6 weeks ago, saved the environment (in rstudio), but when I use the same data and run the geneScore function again (which combines the differential expression and differential splicing scores linearly by default), I get completely different integrated gene score values (which also produce rubbish in the downstream analysis). Does anyone have any idea what might be different? I'm running exactly the same script commands on exactly the same count and permutation data. I'm completely puzzled.

Thanks
Tom