We have performed a genome-wide screen for recent adaptive transposable element insertions in Drosophila melanogaster. While previous studies included only a subset of the transposable element insertions present in the reference genome, we have now analyzed all the euchromatic insertions in three out-of-Africa populations, North Carolina (US), Bari (Italy) and Stockholm (Sweden), and in one African population from the ancestral range of the species. We identified 41 candidate adaptive TEs with significantly different frequencies within and outside of Africa. One of the putatively adaptive insertions identified is a roo solo-LTR retrotransposon located in the 5'-UTR of CG18446, a candidate cold-stress response gene. We found that besides FBti0019985, there are another eight transposable elements inserted in the proximal promoter region of CG18446. All nine insertions are solo-LTRs that belong to the roo family. We found that different insertions have different molecular and functional consequences. The exact position where the transposable elements are inserted matters, as they all showed highly conserved sequences but only two of the analyzed insertions provided alternative transcription start sites, and only the FBti0019985 insertion consistently affects CG18446 expression. The phenotypic consequences of the different insertions also vary: only FBti0019985 was associated with cold-stress tolerance. Interestingly, in the only previous report of transposable elements inserting repeatedly and independently in a promoter region in D. melanogaster, the insertions were also located upstream of a stress response gene. Our results suggest that functional validation of individual structural variants is needed to resolve the complexity of insertion clusters.