Exporting from SSRS is not great, and although you are staying in the microsoft range of products, complications do occur. If you have extra resources you could always splash out and buy an add-on for SSRS that performs exports better such as OfficeWriter from www.softartisans.com which provides much more control over Excel output.
From my experience its basically headers (either column or page) and footers which cause the issue If any of these headers / footers overlap with data columns in your report, you can find that the exprted version of the report has merged cells.
Also checks columns next to each other (simple I know) to make sure there is no overlap in the rpeort designer in BIDS.
I was having this problem with a 3-line header that was centered. It merged columns on either side of where the header text began and ended.
I was able to get around this by creating a textbox with the page header text that spans the full width of the page AND then giving it a background color. I know it sounds silly, but this a way to explicitly tell it to create a header that was the full width. My previous background color was transparent, and I changed it to White, and it worked.