EBS volumes are portable between instances running different operating systems but this does not mean the underlying file system format will be compatible. EBS is a block level storage device. The volume must be formatted with a file system which may or may not run across different EC2 instances based upon the OS of the instance.
Moving between Linux and Windows file formatted EBS formatted volumes were most of the compatible issues may arise. NTFS and EXT4 are some of the most common file system formats.
An option is to used NTFS as your 'master' file system. Then use a utility like ntfsprogs (http://en.wikipedia.org/wiki/Ntfsprogson) to use the EBS volume for both Windows and Linux instances. If you don't need writing on Linux, you can mount the NTFS drive and read it on Linux . Linux can natively read NTFS but it can not write to NTFS drives natively.
The other option is to use EXT4 (or another Linux file system) as your 'master' file system. For example, EXT4 is not natively supported on Windows. Good discussion here:
Also, ext2fsd (http://www.ext2fsd.com) a proven solution for reading EXT4 from Linux. For those that don't need NTFS, sharing filesystems between Windows and Linux can be done using exFAT. Another potential solution that supports reading and writing to NTFS on Linux is: http://sourceforge.net/projects/ntfs-3g/