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init_bugs2: fix issue #1017 and other issues pointed out by Chris and… #414

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Job	Run time
setup	44m 9s
build (Ifremer1)	1m 34s
build (NCEP_st2)	1m 21s
build (NCEP_st4)	1m 28s
build (ite_pdlib)	1m 35s
build (NCEP_st4sbs)	1m 21s
build (NCEP_glwu)	1m 20s
build (OASACM)	1m 22s
build (UKMO)	1m 25s
build (MULTI_ESMF)	1m 8s
	56m 43s