It's a common story: SquareSoft contracted out the port job to Eidos and Eidos screwed up. But I think that story is wrong.
Before I continue, I must point the difference between Square Co. and SquareSoft, Inc. The first was the Japanese company that merged with Enix to form Square-Enix. The second was the North American subsidiary.
1. Press releasesPrior to the release of the PC port, there were at least a few articles about it. I have two here, an announcement and an article about the licensing of the XG synth from Yahama.
Both articles call Square Soft the developers of the port (as distinct from Square Co. the original developers of the Playstation version) and call Eidos the one publishing or marketing the PC port.
Release announcement
(for Europe?):
http://www.thefreelibrary.com/Eidos+and+SquareSoft+Announce+the+Release+of+Final+Fantasy+VII+for...-a050113699
http://www.ff7citadel.com/press/pr_pc.shtml
Yahama article:
Freelibrary copy: http://www.thefreelibrary.com/Yamaha+Corporation+licenses+its+XG+Soft+Synthesizer+to+Square+Soft...-a020504481
Archived Yahama website page: http://web.archive.org/web/19981205100929/http://www.yamaha.co.jp/english/news/98042102.html
2. CreditsThere's a noticeable lack of programmers listed under the two Eidos sections in FF7PC's credits. Nor are there any of Eidos' subsidaries listed. Square Soft, Inc. does have programmers listed.
Senior Software Engineers
Anthony Ignacio
Son Ton
Software Engineers
"William" Feng chen
Scott Conventon
Jay Fong
Kazumasa Fusya
Akintunde Omitowoju
Rajiv Patel
Yoshinori "Goro" Uenishi
One of the probably better-known-today programmers, Jay Fong, lists his work on FF7 for SquareSoft on his LinkedIn page.
What's more likely? That SquareSoft tried to steal all the credit for the port with several programmers going along with the charade, but failed? Or that people wrongly blamed the publisher? Maybe because they couldn't doubt the name “Squaresoft” that they associated with all Square's games or because they only interacted with the publisher when dealing with support?