Multiple transcripts matching same gene in de novo assembled RNA-seq data, but FPKM values vary?
If the quantification is done at the transcript level, each identified transcript of a given gene will have a different number of reads attributed to it, hence a different RPKM value.

For the subsequent analysis, you can continue at the transcript level.

I think you cannot sum the FPKM values directly, because they are inversely proportional to the transcript lengths ("K" stands for "by kilobase"). If you want to do the subsequent analysis at the gene level and use FPKM values, you would have to multiply the FPKM values of the transcripts by the corresponding transcript lengths before summing. Then you will have to divide this sum by the gene length, or something like that.