Problem accessing linux

Hi,

Whenever I change some of the options for the kernel (like enabling serial port and disabling ehternet for example) or add my application programs to a filesystem and upload them, I cant seem to run uclinux. After typing in the username, it doesnt really go to the next step of asking the password. After some warning about the jtag being possibly unstable, the cursor just goes and sits on the next line (not the prompt - i cant execute any commands if i type). However it works fine with the default settings used with the microtronix guides. Any ideas as to why this happens? Any help is appreciated.