I've always had the interpretation that Cloud's memory problems are the result of him deceiving himself, combined with mako poisoning. I know he was injected with Sephiroth cells, so Jenova/Sephiroth could influence him as we see in game, but if Jenova was deliberately messing with his mind, shouldn't his memories be more... negative?
I imagine Jenova would want Cloud to feel hopeless, rather than confused. This is why I doubt whether Jenova was involved when Cloud created his false personality upon meeting Tifa in Sector 7. Cloud imagines a idealized past for himself, which allows him to live and interact with others for a while. The only motivation needed here is Cloud's own insecurity, Jenova doesn't need to be invoked at all IMO. Jenova would want him to be as ineffectual as possible, to remain catatonic forever. She wouldn't want him to have ANY persona if she had that much control over his mind. (And I know Tifa is involved in reviving him)
If Jenova was really affecting Cloud's memories of his mom, wouldn't she want to change things so that Caudia seems dissapointed? I mean, it's a pretty wholesome interaction all things considered. If Jenova is interferring to take out all references of Tifa, it doesn't seem like that big of a deal.
Again, if Jenova had this much control over Cloud's mind, she'd want him to feel hopeless, not confused.