The read.table() function uses the number symbol ("#") as a comment character and hence data after "#" is truncated. One way to avoid truncation when using read.table(), which applies to all types, is to turn off the interpretation of comment characters as shown in the this example:
frame<-try(read.table(IN,header=FALSE,sep="\t", quote="",nrows=1,comment.char=""),silent=TRUE)