I too am more of a scientist/skeptic than a mystic, and I think thats why pragmatic dharma works for me as a hobby/lifestyle. It really is a series of first-person claims with experiments you can do to verify them for yourself.
Disturbing feelings, at least for me, usually indicate I've hit a new, unexplored, and interesting territory in my own brain. In other words, progress. As you move along the path of insight, expect lots of unsettling/hard to explain occurrences.... entire religions or worldviews have been founded on the disturbances therein.
I've personally never had a strong deja vu experience like that one scene in the Matrix...
and I'll decline to respond in more detail because I'm never going to beat out these parapgraphs from wikipedia:
Scientific research
The psychologist Edward B. Titchener in his book A Textbook of Psychology (1928), wrote that déjà vu is caused by a person getting a brief glimpse of an object or situation prior to full conscious perception, resulting in a false sense of familiarity.[2] The explanation that has mostly been accepted of déjà vu is not that it is an act of "precognition" or "prophecy", but rather that it is an anomaly of memory, giving the false impression that an experience is "being recalled".[3][4] This explanation is supported by the fact that the sense of "recollection" at the time is strong in most cases, but that the circumstances of the "previous" experience (when, where, and how the earlier experience occurred) are quite uncertain or believed to be impossible. Likewise, as time passes, subjects can exhibit a strong recollection of having the "unsettling" experience of déjà vu itself, but little or no recollection of the specifics of the event(s) or circumstance(s) they were "remembering" when they had the déjà vu experience. In particular, this may result from an overlap between the neurological systems responsible for short-term memory and those responsible for long-term memory (events which are perceived as being in the past). One theory is the events would be stored into memory before the conscious part of the brain even receives the information and processes it.[5] But this has been downplayed as the brain would not be able to store information without a sensory input first. Another theory suggests the brain may process the sensory input as a memory, and therefore during the event one believes it to be a past memory, yet it is only a memory-in-progress; which is how the brain perceives life. In a survey Brown (2004) had concluded that approximately two-thirds of the population have had déjà vu experiences.[6]
Memory-based explanations
The similarity between a déjà-vu-eliciting stimulus and an existing, but different, memory trace may lead to the sensation.[7][12] Thus, encountering something which evokes the implicit associations of an experience or sensation that cannot be remembered may lead to déjà vu. In an effort to experimentally reproduce the sensation, Banister and Zangwill (1941)[13][14] used hypnosis to give participants posthypnotic amnesia for material they had already seen. When this was later re-encountered, the restricted activation caused thereafter by the posthypnotic amnesia resulted in three of the 10 participants reporting what the authors termed "paramnesias". Memory-based explanations may lead to the development of a number of non-invasive experimental methods by which a long sought-after analogue of déjà vu can be reliably produced that would allow it to be tested under well-controlled experimental conditions. Cleary[12] suggests that déjà vu may be a form of familiarity-based recognition (recognition that is based on a feeling of familiarity with a situation) and that laboratory methods of probing familiarity-based recognition hold promise for probing déjà vu in laboratory settings. A recent study that used virtual reality technology to study reported deja vu experiences supported this idea. This virtual reality investigation suggested that similarity between a new scene's spatial layout and the layout of a previously experienced scene in memory (but which fails to be recalled) may contribute to the deja vu experience [15][15]. When the previously experienced scene fails to come to mind in response to viewing the new scene, that previously experienced scene in memory can still exert an effect--that effect may be a feeling of familiarity with the new scene that is subjectively experienced as a feeling of deja vu, or of having been there before despite knowing otherwise. Another possible explanation for the phenomenon of déjà vu is the occurrence of "cryptomnesia", which is where information learned is forgotten but nevertheless stored in the brain, and similar occurrences invoke the contained knowledge, leading to a feeling of familiarity because of the situation, event or emotional/vocal content, known as "déjà vu".
http://en.wikipedia.org/wiki/D%C3%A9j%C3%A0_vu#Scientific_research