Change the dimensions by going to the Terminal Menu > Window Settings. Click on the pull down window in the Terminal Inspector, and choose "Window". Now you can resize using the pixel values. Now, click at the bottom on "Use Settings as Default". Now, quite Terminal and relaunch. It should be visible now. If not, you can repeat the procedure above, and then before quitting, go to File > Save. When the dialog box pops up, click "Open this file when Terminal starts up". Then click Save. Hopefully that'll do the trick for sure.
As I was playing with my terminal to see if I get your problem, I think I stumbled upon the solution. When you change the no. of rows and columns, in the windows settings, then press tab so that the cursor comes below into the box named 'title'. Only then hit 'Use as default', and then close that window. If you hit'Use as default' while the cursor is still in rows or columns box, it will only change it temporarily.
NOTE. write stty -a to see your terminal settings after you change it.
write stty_ -g > $HOME/.stty to save the new settings.
Although following the NOTE was not correcting the problem for me.
Anyways, the first paragraph should solve it.
cheers