Here's test:

$ fossil new repo.fossil
project-id: 3eb03c25edc4b03e6b9e64985f25d20363aeda0c
server-id:  f18702b2ee13d9a34b020be3cb096ed65f32e1ec
admin-user: dmitry (initial password is "2affdf")

$ mkdir repo
$ cd repo
$ fossil open ../repo.fossil 
$ echo "First" >> myfile.txt
$ fossil add myfile.txt 
ADDED  myfile.txt

$ fossil commit -m "lowercase"
New_Version: 7a77d8c7c80e239225351d4a9b9e9d02c591ebdf

$ mv myfile.txt MyFile.txt
$ ll
total 24
-rw-r--r--  1 dmitry  staff     6 Jan 22 13:11 MyFile.txt
-rw-r--r--  1 dmitry  staff  7168 Jan 22 13:11 _FOSSIL_

$ fossil changes
$ fossil addremove
ADDED  MyFile.txt
added 1 files, deleted 0 files

$ fossil commit
/usr/bin/vim "/Users/dmitry/ST/repo/ci-comment-A85BD1C98500.txt"
New_Version: 3fb2e205f8dad54fbac31a68177648d115ca7860

$ rm *
$ fossil open ../repo.fossil 
MyFile.txt
project-name: <unnamed>
repository:   /Users/dmitry/ST/repo.fossil
local-root:   /Users/dmitry/ST/repo/
project-code: 3eb03c25edc4b03e6b9e64985f25d20363aeda0c
server-code:  f18702b2ee13d9a34b020be3cb096ed65f32e1ec
checkout:     3fb2e205f8dad54fbac31a68177648d115ca7860 2011-01-22 12:12:36 UTC
parent:       7a77d8c7c80e239225351d4a9b9e9d02c591ebdf 2011-01-22 12:11:33 UTC
tags:         trunk
comment:      Renamed. (user: dmitry)
$ ll
total 24
-rw-r--r--  1 dmitry  staff     6 Jan 22 13:13 MyFile.txt
-rw-r--r--  1 dmitry  staff  7168 Jan 22 13:13 _FOSSIL_

Here's manifest of the second commit:

C Renamed.
D 2011-01-22T12:12:36.278
F MyFile.txt 7322e1fd19fd2986254c38eb418971859ede506d
F myfile.txt 7322e1fd19fd2986254c38eb418971859ede506d
P 7a77d8c7c80e239225351d4a9b9e9d02c591ebdf
R 342c091c43d8964d553678092b8218e7
U dmitry
Z cde393ff1422550babdc8a5951aa06d1

anonymous added on 2011-01-22 14:25:40 UTC:
I've made the same test as you and I reproduce everything. But also, I tried the following, may be those extra info can be usefull:

• I copy the fossil file to another OS which have case sensitive filesystem
• I've made a checkout (so I got the 2 files)
• I've edit both of them with different content and then commit

# cat myfile.txt
First file, edited

# cat MyFile.txt
Fist file, with capitals, edited

• I copy back the fossil file to my osx machine with case insensitive, made a checkout, and then I got the following:

meeks-mbp:repo $ fossil open ../test.fsl 
MyFile.txt
overwrite /Users/meeks/fossil/test/repo/myfile.txt (a=always/y/N)? y
myfile.txt
WARNING: manifest checksum does not agree with disk
project-name: <unnamed>
repository:   /Users/meeks/fossil/test/test.fsl
local-root:   /Users/meeks/fossil/test/repo/
project-code: 7dcace824b7b4318bec9a6f80ba2a00fd43215ff
server-code:  6cd5d13657fb215e96caeff6f551584865e6622e
checkout:     c9e1c25a26f1e06694aa947053464db31e854f6d 2011-01-22 14:09:04 UTC
parent:       74671ab018da4f0f288f20cb6d2f1cb21893f084 2011-01-22 14:06:04 UTC
tags:         trunk
comment:      lil changes (user: meeks)
meeks-mbp:repo $ ls
MyFile.txt  _FOSSIL_

And what's strange, I got the file with capital letters, but the content of the one without:

# ls
MyFile.txt  _FOSSIL_

# cat MyFile.txt
First file, edited

anonymous added on 2011-01-22 15:09:45 UTC:
Actually. Answering no to this line:

overwrite /Users/meeks/fossil/test/repo/myfile.txt (a=always/y/N)?

Keep only MyFile.txt with proper content. Answered yes produce MyFile.txt only but with content overwritten with content of myfile.txt...