The variable determining the number of lines is available in the configuration file (extension .ct).
The name of the current configuration file you can find at the first panel of the Status Bar (the default is: cryptoterm.ct).
To change the number of lines of the scroll buffer please input the value in the BUFFSIZE variable.
You can find it in the SETTINGS section.
Scroll buffer may be increased max to 2000 lines.

Example:

[SETTINGS]
BUFFSIZE= 2000

will change the buffer size to the 2000 lines.

Note:

In Windows Vista and Windows7 the configuration file is located in user AppData\Local\CryptoTerm 1.3\CryptoTerm folder.