Actually some very good reasons why this is not at all likely:

1) All Genetically Modified plants are exhaustively tested for any possible such interaction or negative effect. Any activity against bees would be obvious and noted.

2) There are only a few crops that are have been genetically engineered and are being grown commercially. The major such crops are corn, soybean, and cotton with smaller amounts of a few additional crops. These crops are not primary sources for bees to feed on.

3) The noted declines for bees are occurring throughout the world but GE crops are not grown in many area that are experiencing the problems with declines in bee populations.

4) There is no technical reason based on the known activity of genes that have been engineered into plants to suspect that there would be any effect on bees.

5) Causes for the declines in bee populations are known such as mites, and varioius diseases -fungal, bacterial and viral.

6) There is no evidence for GE crops having negative effects on bees - and yes they have been tested.

7) Finally, what many people do not realize is that GE plants are not so different from other plants. They typically have one very well understood gene that is added to their genome and the expression of that gene and its protein have been exhaustively studied.
Crop plants produced by "ordinary" breeding have ~20,000 unknown genes - essentially none of which have been tested...