First, we would really need to see some of the data to see why you are getting the Unitialized warning. Second, you are clobbering over your file for every loop pass in the bottom foreach. You already opened the file for writing at the start of the script, there is no need to re-open it in the foreach loop. This is why you are losing your HTML header info.

Remove first line that closes your output file and move it to the end of the script. Likewise, remove the open and close lines in the foreach loop.

L-LL-L--L-LL-L--L-LL-L--
-R--R-RR-R--R-RR-R--R-RR
B--B--B--B--B--B--B--B--
H---H---H---H---H---H---
(the triplet paradiddle with high-hat)