I don't think there is any difference in meaning. The two can be used interchangeably, though Alex is right that "despite" sounds just slightly more formal.
After "despite" or "in spite of," you can use either a noun (or noun phrase or pronoun) or a gerund (or gerund phrase). For example:
"Despite her fear of heights, she climbed up the ladder." ("her fear of heights" is a noun phrase; the main noun is "fear")
"Despite being afraid of heights, she climbed the ladder." ("being afraid" is a gerund phrase)
"In spite of having seen the movie twice, he did not understand the story." ("having seen" is a gerund phrase)
"In spite of the cold, they went outside." ("the cold" is a noun phrase; "cold" is the noun)
"Despite the fact that he knew the answer, he did not raise his hand." ("the fact that he knew the answer" is a noun phrase; "fact" is the main noun)
(Edited: I originally said "participle" instead of "gerund," but I've checked some grammar sources and it seems that the -ing phrases after "despite" are gerunds, not participles. In any case, you need a verb that ends with -ing. The -ing word will usually describe the subject of your sentence, which makes it seem more like a participle to me, but you can't use participles that end in -ed. You need an -ing word. So it is probably correct to regard these as gerunds.)