Exactly the same thing happens to me but I am trying to dual-boot Win98SE and Win 10. Both are completely installed, but the only way I can get into Win 98 is via the startup disk and a reinstall, and the only way I can then get back into Win 10 is by running fdisk in Win 98 and making Disk 2 active again. Both OSes show up to choose from, but only Win 10 actually opens. Your programme even the latest ed. of EasyBCD 2.3 does not set in a proper path for Win 98, but I land at a curious prompt like a DOS prompt. Or else the PC complains of a missing GRUB file. Windows boot loader shows only Windows 10.
Did you install the legacy OS at the start of the HDD ?
The ability to dual boot began with XP (SP1 iirc).
MS OS's prior to that have hard-coded expectation in the OS loader that the OS resides at the very start of the HDD.
Probably not: I just took all the advice I could get, defragged my 1TB SSD and carved out 20GB formatted in FAT32. I'm not sure how to do it otherwise, unless the legacy OS had gone in first. But I do know that people are managing to put win 98 in on top of Win 7 doing nothing fancier than making space for it as I did, and then dual-boot. I am beginning to suspect that upgrading 7 to 10 before putting in 98 is the hitch. I could try starting with 7 instead in another PC (both mine are now upgraded to 10). Though perhaps subsequently upgrading to 10 may destroy the dual-boot. 10 appears to boot differently from all previous OSes. These people NIXSYS - IT for Business and Custom Build Computers and Servers offer sundry legacy arrangements at a price. But what I am after is a really powerful modern 64-bit PC with 98 on the side. I need the latter for a v. old Hebrew-Arabic-Greek DOS-based programme; and fax with distinctive ring would also come in handy, to filter out a lot of nuisance calls on my fax no.