I just want to add here that I also experienced the same thing where com.apple.Boot.plist is ignored by bootloader. Themes, dsdt.aml & extensions are loaded/read correctly when booting. Because of the Boot.plist files is ignored, I have to enter the flags manually (e.g. arch=i386). This is on MBR partition & Chameleon 2 RC5. Just in case the Boot.plist file is corrupted, I already replaced it with the one confirmed working from the other computer. I don't know why Boot.plist is the only file is ignored by bootloader because themes, dsdt.aml & extensions which also in /Extra folder can be loaded without any problem.
I have two computer (MBR) which use Chameleon 2 RC5. The first one which is working, OSX is installed at hd(0,3). While the second one which have this Boot.plist problem, OSX is installed at hd(0,4). Both partition are primary partition.
com.apple.Boot.plist:-
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>Kernel</key>
<string>mach_kernel</string>
<key>Kernel Flags</key>
<string>arch=i386</string>
<key>Legacy Logo</key>
<string>Yes</string>
<key>RestartFix</key>
<string>No</string>
<key>SMBIOSdefaults</key>
<string>Yes</string>
<key>Timeout</key>
<string>5</string>
</dict>
</plist>
diskutil list:-
/dev/disk0
#: TYPE NAME SIZE IDENTIFIER
0: FDisk_partition_scheme *320.1 GB disk0
1: DOS_FAT_16 DellUtility 41.1 MB disk0s1
2: Windows_NTFS RECOVERY 15.7 GB disk0s2
3: Windows_NTFS OS 152.3 GB disk0s3
4: Apple_HFS OSX 152.0 GB disk0s4
Extra folder:-
total 1600
drwxr-xr-x 13 root wheel 442 Nov 3 09:25 .
drwxrwxr-t 35 root admin 1258 Nov 2 23:29 ..
drwxr-xr-x 11 root wheel 374 Nov 3 09:25 Extensions
-rw-r--r-- 1 root wheel 669131 Nov 3 09:25 Extensions.mkext
drwxr-xr-x 6 root wheel 204 Sep 10 01:00 Themes
drwxr-xr-x 3 root wheel 102 Sep 17 20:42 Util
drwxr-xr-x 2 root wheel 68 Sep 17 20:42 bin
-rw-r--r--@ 1 root wheel 469 Nov 2 23:44 com.apple.Boot.plist
-rwxr-xr-x 1 root wheel 42525 Nov 3 08:06 dsdt.aml
-rwxr-xr-x 1 root wheel 42380 Sep 20 20:41 dsdt.aml.backup
-rwxr-xr-x 1 root wheel 42428 Nov 3 08:05 dsdt.aml.backup02
-rwxr-xr-x@ 1 root wheel 549 Sep 10 01:01 smbios.plist
-rwxr-xr-x 1 root wheel 264 Sep 10 01:05 updateExtensionsMkext