The updated version of Fragstats, that works with ArcGIS 10, is a bit temperamental. I would recommend converting your raster data to an ERDAS Imagine (img) format. The raster(s) also need to be a single band "signed" 8, 16, or 32 integer. Another recommendation is, that because historically zero values have been converted to 1 on the fly, it is best to avoid zero values in your raster. It is good practice for your projection to also be in meters, which is assumed in Fragstats.
You can convert your raster and specify output type in ArcCatalog by right-clicking the raster and selecting Export > Raster to Different Format in the context menu. In the resulting dialogue, name your output raster with an "img" extension and select "8_BIT_SIGNED", "16_BIT_SIGNED" or "32_BIT_SIGNED", depending on the range of values in your raster, in the pixel type dropdown menu.
8_BIT_SIGNED�??A signed 8-bit data type. The values supported can be from -128 to 127.
16_BIT_SIGNED�??A 16-bit signed data type. The values can range from -32,768 to 32,767.
32_BIT_SIGNED�??A 32-bit signed data type. The values can range from -2,147,483,648 to 2,147,483,647.