A lot of problems to begin with.

» You are accessing form elements the wrong way. Read this.

» prompt() returns a string and you are treating it as a number which in itself is introducing a lot of problems.

» setTimeout() takes it's second parameter as milliseconds and not seconds.

» I see a lot of needless calculations going on in showTime() function. Don't touch the DOM unless absolutely necessary. For eg. since we know that the value of the 'hour' text field would only change after 60 minutes, there is no point in updating it every second.

» In javascript, numbers are represented using 64 bit double precision format as per the IEEE floating point standards. Showing the amount of 'seconds' left in decimals would be not desirable. Use the toFixed() function of Number to get away with those extra digits after the dot.

Follow the suggestions, format and indent the code and come up with a fresh solution.