The Flynn effect does not affect scores only a year apart by much, when you are talking about the same instrument, but it affects this WISC-IV/WPPSI-IV discussion because, as was noted upthread, the WISC-IV administration occurred in 2013, when the norms were 10 years old (probably really 11, as the standardization data would have been collected many months, even up to a year, before the publication date), and in the last year before being superseded by the next edition (the WISC-V was released less than a month ago). The WPPSI-IV administration, OTOH, occurred in 2014, the year of its publication, when the norms were less than a year old.
The issue of the Flynn effect is more descriptively labeled as norm obsolescence, which clarifies that it is not when the tests are administered per se that affects their standard scores, but when in the lifespan of the norms they are administered.
And yes, it's the structures of the tests that are not one-to-one comparable, although attempts were made to make them so. The global/full scale score is probably the place with the closest match. The Verbal tasks are very similar, so one would expect a better relationship. The perceptual tasks are not exactly the same. Then, of course, is the question of what tasks best assess the theoretical cognitive processes at which developmental levels. It's possible that the same task may measure different skills at different points.
Most importantly, when comparing WPPSI and WISC scores of any kind, one is usually comparing very young children with school-age children. The younger child usually is expected to have a less-stable result. If you are measuring the same child on both instruments, this close together in time, then one of the administrations must have been done in the top of the WPPSI age range (test ceiling effects come into play for higher functioning students--not necessarily that high, either, just above average), and the other administration must have been done in the beginning of the WISC age range (now floor effects become a factor, except with fairly high functioning students).