Yes, the issue could be the windows file system size or its way of dealing with long file names. But the failure in reading might even be due to Colinux. Windows has never complained in sending the data to Colinux but CoLinux always complains in not able to read the data. The Colinux change log does mention about I/O errors.
Was going through this link on Working with File Systems which says:
If you use a large number of files in an NTFS folder (300,000 or more), disable short-file name generation, especially if the first six characters of the long file names are similar.
Every time you create a file with a long file name, NTFS creates a second file entry that has a similar 8.3 short file name. A file with an 8.3 short file name has a file name containing 1 to 8 characters and a file name extension containing 1 to 3 characters. The file name and file name extension are separated by a period.
If you have a large number of files (300,000 or more) in a folder, and the files have long file names with the same initial characters, the time required to create the files increases. The increase occurs because NTFS bases the short file name on the first six characters of the long file name. In folders with more than 300,000 files, the short file names start to conflict after NTFS uses all the 8.3 names that are similar to the long file names. Repeated conflicts between a generated short file name and existing short file names cause NTFS to regenerate the short file name from 6 to 8 times.
To reduce the time required to create files, use the fsutil behavior set disable8dot3 command to disable the creation of 8.3 short file names. (You must restart your computer for this setting to take effect.) For more information about disabling 8.3 short file names, see “MS-DOS-Readable File Names on NTFS Volumes” later in this chapter.
If you want NTFS to generate 8.3 names, improve performance by using a naming scheme in which long file names differ at the beginning of the name instead of at the end.
But again, disabling 8.3 filenames systemwide seemed a bit drastic, and could lead to other unexpected problems elsewhere. So, for now we have not done the disabling.