The company I work for was given grant money by the Canadian government to invest in research and development. I was told by my boss that because xx% of my wage was paid by the goverment that I was required to do community work that supported Universities (this was a lie). I wrote a substantial piece of software that required me to pay for the development tools. More than half of the work was done at my home unpaid. The software was open sourced with my bosses approval. During a routine IT audit at our facility corporate IT found out about the project and demanded it be taken down immediately and that there was no agreement with the government whatsoever.

I never kept track of the amount of time that I worked on the project since it was open source work and so couldn't accurately say how may hours were involved but it was over the course of a couple of years and was in the thousands of hours researching and writing / testing code. Needless to say the company refused to pay me for anything because I couldn't prove exactly how many hours I worked on the software. The story gets even more crazy but it's too long to go into.

Any thoughts on how you would handle something like this?