...Someone knows how to fix this?
Sorry, I have not seen that and do not have a Windows machine to test it. Have you tried another computer? That will tell you if the trouble is with the Digispark, or with the computer.
And also, how can I prevent my script to be running the time the upload is completed?
You can't - the process of uploading the sketch (script) is completed by resetting the microcontroller. The reset will cause the ATtiny85 to launch the bootloader which waits for five seconds and, if there is no sketch waiting to upload, will continue on with running the sketch currently in it's program memory. This is by design, and is the basic operation of all Arduinos. The only way to prevent it is to immediately (well, within the five second wait time) remove power and not apply power again until you are ready for it to run your sketch.
While you cannot prevent the sketch from running, you could attach a pushbutton switch and have your sketch start out by waiting for the button to be pressed, and then running the rest of the sketch. That might do what you want.
