I couldn't use reactome.db (it is not exported on the NAMESPACE, but maybe should it be generated somehow in zzz.R), neither the reactome_dbInfo() work but now it seems that genes are correctly mapped to the pathways:

> install.packages("reactome.db_1.0.59.tar.gz", repos = NULL)
Installing package into ‘/home/user/R/x86_64-pc-linux-gnu-library/3.3’
(as ‘lib’ is unspecified)

* installing *source* package ‘reactome.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (reactome.db)
>
> library(reactome.db)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
    duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
    is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
    Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    colMeans, colSums, expand.grid, rowMeans, rowSums
> select(reactome.db, key = "3855", keytype = "ENTREZID", columns = "REACTOMEID")
Error in select(reactome.db, key = "3855", keytype = "ENTREZID", columns = "REACTOMEID") :
  object 'reactome.db' not found

>  ls("package:reactome.db")
 [1] "reactome"              "reactome_dbconn"       "reactome_dbfile"      
 [4] "reactome_dbInfo"       "reactome_dbschema"     "reactomeEXTID2PATHID"
 [7] "reactomeGO2REACTOMEID" "reactomeMAPCOUNTS"     "reactomePATHID2EXTID"
[10] "reactomePATHID2NAME"   "reactomePATHNAME2ID"   "reactomeREACTOMEID2GO"
> reactome_dbInfo()
                name                                     value
1           DBSCHEMA                               REACTOME_DB
2    DBSCHEMAVERSION                                        59
3         SOURCENAME                                  Reactome
4          SOURCEURL http://www.reactome.org/download/current/
5         SOURCEDATE                                2017-02-27
6 Supporting package                             AnnotationDbi
7            Db type                                ReactomeDb
> reactome_dbschema()

Warning messages:
1: In file(con, "r") :
  file("") only supports open = "w+" and open = "w+b": using the former
2: In max(ii) : no non-missing arguments to max; returning -Inf
> xx <- as.list(reactomeEXTID2PATHID)
> xx[["3855"]]
[1] "1266738" "6805567" "6809371"

If you need more help testing it, I am glad to help.

I noted some other changes on the new version which I don't know which is the cause, maybe the mapping or the updated of the data.

There are now less genes in reactomeEXTID2PATHID, from 65445 there were previously to 27956 genes, also from 17151 pathways(?) in the previous version now there are 1932.

In the reactomePATHNAME2ID now there are 21998 pathways but 9 of the pathways of reactomeEXTID2PATHID are not there and there are 255 pathways annotated in pathNAME2ID not annotated in EXTID2PATHID.

In the latest version :

reactomeEXTID2PATHID reactomeGO2REACTOMEID  reactomePATHID2EXTID
                27956                  1791                  1932
  reactomePATHID2NAME   reactomePATHNAME2ID reactomeREACTOMEID2GO
                 2176                 21968                 10554

Previously:

> reactomeMAPCOUNTS
 reactomeEXTID2PATHID reactomeGO2REACTOMEID  reactomePATHID2EXTID
                65445                  1796                 17151
  reactomePATHID2NAME   reactomePATHNAME2ID reactomeREACTOMEID2GO
                20800                 20767                 51734