I've had tables with >100k rows so the 1000-row truncation you describe is caused by something else.
I'd open the raw data file and look at rows 1000 and 1001 to see if there's something unusual that may be preventing rows 1001-end from being read-in.
Of course the command you're using to read in the data could also be limiting the number or rows.
The "Extended Capabilities" section of the documentation for Tables shows how to use Tall Arrays if you run out of memory when construction the table.
