A new release of the Zip PECL package has been made according to this post on Pierre-Alain Joye's blog today. The main update in this release is to counteract a Windows bug that's interfering with binary file opens.
The issue is actually a windows bug. No matter if I give or not the "b" flag to fopen, the write operations are not binary safe. It seems to be a known issue as many projects use the same trick.
The problem comes up when PHP forces the binary mode in SAPI and CLI, making the binary writes to a file non-binary safe no matter what. Pierre is also asking for help from anyone out there with any information/bug reports/references about this issue that would yield something useful.