you type dim(A) [or length(A) if it is a vector] and see that it only loads the first 100.000?
Thats very strange, I've never had any problems of the sort and I have worked with data frames of about 1e+06 x 8 elements in R. R should be able to handle even bigger files see:
Do you get any error messages? Hows your system specs?
The problem might be related to read.table however I doubt.
You can try read.csv() or read.csv2().
Also have you tried posting your question to the R-Help mailing list?
They will be more than happy to explain (in detail) what could be wrong.
Before you try them however please search the archives: