Hello,
The FAT32 format has file limitations; there is no way around it. It will work for both Mac and PC but as you are finding there are limitations on file size.
I'd recommend using exFAT format. It will work for both if your OS is up to date.
"exFAT (Extended File Allocation Table) is a proprietary file system designed especially for flash drives developed by Microsoft, which has applied for patent protection. It is supported in Windows XP and Windows Server 2003 with update KB955704, Windows Embedded CE 6.0, Windows Vista with Service Pack 1, Windows Server 2008,[5] Windows 7, Windows Server 2008 R2 (except Windows Server 2008 Server Core), Mac OS X Snow Leopard starting from 10.6.5, Mac OS X Lion and Mac OS X Mountain Lion."
From the Wikipedia article.
http://en.wikipedia.org/wiki/ExFAT