This is similar to read.csv row.names and to https://stackoverflow.com/questions/12425599/duplicated-row-names , but I do not see answers that help.
Problem: Trying
I used the following code:
lm.table <- read.table("file name", header=TRUE, row.names=NULL)
This added a column to the left with numbered row names, but I didn't find that the column names were shifted. Could it be that your column names still matched the right columns, but the R output made it look like the names had shifted?