The situation that you are describing — where the Eggbot hardware is working, but yet it cannot connect through Inkscape — is rare. (We do a lot of tech support for Eggbot kits. If something can go wrong, we have seen it. This is just about the least common thing that can go wrong.) The most likely situation is that something “unusual” on your computer is blocking access to the serial port. That could be as simple as leaving a putty connection open, it could be anti-viral/malware software on your computer blocking ports, it could be other USB devices, especially ones that take special drivers. (We have seen cases where uncommon USB devices have caused conflicts.) Can you think of anything that might be causing an issue of that type?
We have also on occasion heard of intermittent problems due to USB cable or hub issues. These have sometimes presented as Eggbots that show up in the device manager, but can’t connect from Inkscape, or which print for a while and then stop. If you have a different USB cable that you can try (or if you are using a hub or extension) you might try to see if anything makes a difference.
