Windows partition utility does not agree with fdisk

The background for this is here. Tl;dr: I created 3 primary partitions (SYSTEM, C:, shared data) and two logical (/boot and /) for a dual boot system, and ran into issues with chainloading from win7 with EasyBCD. To troubleshoot, I simplified the setup to 3 primary partitions, and am now trying to go back... but can't!
Method:
- Delete all volumes/partitions after C:
- Create primary partition of ~100G, NTFS formatted (shared data)
- Create logical partition of 256M, unformatted (/boot)
- Create logical partition with remaining space, unformatted (encrypted /)
I used the built-in win7 partition utility for this, and it looks like it worked: screenshot
My first alert was the fact that Minitool Partition Wizard didn't agree with win7: screenshot
In fact, trying to create logical partitions with Minitool reports that the operation was successful, but as soon as it completes they turn back into unallocated space. I actually tried this first and then went with the win7 utility as I thought something was wrong with Minitool. I'm starting to think it's the other way around and that Minitool sees the correct state and win7 is wrong. That diagnosis comes from the output of fdisk via booting an Arch installation image:
Invalid flag 0x7d9b of EBR (for partition 5) will be corrected by w(rite).
Disk /dev/sda: 238.5 GiB, 256060514304 bytes, 500118192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0x1e6513b3
Device Boot Start End Sectors Size Id Type
/dev/sda1 * 2048 2101247 2099200 1G 7 HPFS/NTFS/exFAT
/dev/sda2 2101248 172433407 170332160 81.2G 7 HPFS/NTFS/exFAT
/dev/sda3 172433408 387473407 215040000 102.6G 7 HPFS/NTFS/exFAT
/dev/sda4 387473408 500115455 112642048 53.7G f W95 Ext'd (LBA)
/dev/sda5 2961659748 5859253686 2897593939 1.4T 65 Novell Netware 386
No idea whatsoever on the type ID assigned to /dev/sda5, nor why it shows as 1.4T. I've tried various things with no success:
- check/fix errors via win7 drive properties (no errors found)
- delete all non-win7 partitions, grow the partition to the full disk, and then shrink back again
- shrink win7 to ~80G, create a single primary partition, boot Arch install media, format with ext4, `dd if=/dev/zero of=file.txt` until full, then delete file
- change order (2 logicals, then primary)
- format the logicals with NTFS upon creation instead of leaving them unformatted
- assigning drive letters upon creating the partitions vs. no drive letter
I'm hesitant to just do everything from fdisk, as I have McAfee Endpoint Encryption and I'm not sure if writing the partition table from outside of windows can possibly ruin anything related to how the startup decryption works. If someone can assure that dd'ing some number of bytes on /dev/sda would allow me to reverse the process (restore said bytes to the beginning of the drive) in the event of any failures, I'd be willing to give that a shot. I know I've dd'd the encrypted MBR in the past and successfully restored it (after trying to install grub instead of the windows bootloader) just fine and been able to boot again. Not sure if messing with the partition table is any different.
Thanks for any suggestions!

Hi Pradhiba and A.H.P,
I got this problem yesterday and I tried all steps mentionned in this message of yours. Just for your information I checked the following points also (maybe it helps you to analyse better the problem):
System Analysis:
1. SE16 T000
2. SE16 RSBASIDOC in both systems
3. SU01 PROFILES
    BWREMOTE       > To be checked
    ALEREMOTE   and profile S_BI-WX_RFC   see note 150315 > To be checked
4. WE20 Partner Profile LS settings in both are OK
    BW outbound RSRQST
            inbound RSINFO RSSEND
    R/3 outbound RSINFO RSSEND
                             inbound RSRQST
    also check 'RSSEND' in R/3
BIDOCTYP = ZSUB161 > To be checked
5. SM59 .. appears to be ok
6. check inconsistency in tables RSISOSMAP and RSOSFIELDMAP
   SE16 BW for table RSISOSMAP
7. SE16 BW for table RSOSFIELDMAP
     no 'T' entries
8. in BW > source system
The remote users for calling and sending data must have the type
   Dialog or CPIC (see Note 161570).
9. Run the report RS_TRANSTRU_ACTIVATE_ALL (activate all BW structures)
10. check entries on the table bdls
Maybe I will re-check all this again today.
In the mean time I will appreciate any other suggestions that you may have about this issue.
Thanks,
PL.
Message was edited by: Paulo Lie
Message was edited by: Paulo Lie

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