From Pali linguistics perspective, both words share the common root jna ("to know"). So jnana literally means "knowledge", while pra- in prajna means "before" and "super", making it into "super-knowledge" or perhaps "proto-knowledge" or even "meta-knowledge".
Traditionally in Buddhism (Tibetan or not), jnana is used to refer to various insights (realizations, recognitions) one gets along the way, while prajna is taken to mean the noumenal aspect of the Ultimate Realization (Enlightenment).
Unfortunately the schools disagree on what exactly it means to be enlightened, and therefore on the exact nature of prajna. Here I'll speak from Mahayana/Madhyamaka perspective, as I understand it.
Most Mahayana schools of Madhyamaka heritage equate prajna with either direct supraconceptual realization of Emptiness ("the ultimate reality") or, taking it a step further, with direct realization of inseparability of "the ultimate reality" and "the conventional reality" (the world as we know it in day-to-day living).
The Chan family of schools traditionally emphasizes the "supraconceptual" part of Realization, for them understanding is incomplete until your really "get it" deep in your guts, so to speak. So when they talk about prajna they mean not as much intellectual understanding of "the two truths", as realization of its practical implications to our life -- and the resulting modus-operandi.
From this realization comes certain skill in dealing with phenomena, now seen as lacking substantial existence. One can jungle alternative designations without getting stuck. This skill, in my understanding, is the prajna proper. At the same time the Realization comes with coemergent compassion towards sentient beings trying to organize their lives around the wrong assumption that reality they deal with is solid and reliable. As well as with clear understanding that a sentient being can't simply jump from its modus-operandi based on innate confusion, to the modus-operandi based on enlightenment. There is time and effort and the right conditions required. This drives even more compassion on the side of the ones acquainted with "the knowledge of the two truths", due to which they see the need to employ upaya or skillful means, to gradually take sentient begins from point A to point B.
This conglomerate of realizations, concerns, considerations, and the resulting behavior is known as "prajna-karuna", the unity of wisdom and compassion.
The reason some teachers may downplay prajna, is because without the water of compassion it is considered a dry understanding of emptiness, lacking life, therefore incomplete. I suppose their praise of jnana could refer specifically to "knowledge of the two truths", which is said to be the root of compassion.
As always in Buddhism, the words are used as designations to refer to some real stuff going on. As long as we know what we are talking about, we won't get confused as to what's what.
