Rows being dropped in R with read.table?

I am loading a table in which the first column is a URL and reading it into R using `read.table()`. It seems that R is dropping about 1/3 of the columns and does not return any errors. The URLs do not contain any `#` characters or tabs (my separator field), which I understand could be an issue. If I convert the URLs to integer IDs first, the problem goes away. Is there something about the field that might be causing R to drop the rows?
Could you provide us with a little sample of the data (from a plain text editor, not after loaded into R)? Are you using any parameters with your read.table() or just the defaults? (PS - thanks to whoever upvoted my answer version of this comment so that I could have enough rep to comment!)

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