I’m not a Studio One expert, but isn’t a “Project” for mastering purposes, while a “Song” is what you are normally working with when using Melodyne? Do you use the same piece of audio for both approaches? And is the audio routing the same in both?
I can’t see why Melodyne should analyze the audio differently depending on the Studio One mode, but do you know that you can always force Melodyne to use a dedicated algorithm? See the corresponding menu.
I have 2 GB RAM. Is this a RAM problem or some settings issue?
Running short of RAM is certainly an issue here. And 2 GB is not an awful lot nowadays. A high CPU load is possibly another issue on your system. Whenever you hear clicks and pops, you should try increasing your audio buffer size. Please see our tips on optimizing your system
for best Melodyne performance.