It appears that the latest cygwin on windows has a newer version of egrep (2.5.4?) that has some problems with the -i (ignore case) option. Some of the sanity checks use the -i option and are failing and giving false sanity errors. Mostly with regards to paths not being full paths.

The errors will look something like:

ERROR: ALT_BOOTDIR must be an Absolute Path Name,
       not a Relative Path Name.
       The current value of ALT_BOOTDIR is
           C:/cygwin/home/ohair/import/WINDOW~1/JDK16~1.0
       Please fix this and continue your build.

A workaround is to replace the patterns $(EGREP) -ci '^([a-z]:)?/' with $(EGREP) -c '^([a-zA-Z]:)?/'

diff --git a/make/common/shared/Sanity.gmk b/make/common/shared/Sanity.gmk
--- a/make/common/shared/Sanity.gmk
+++ b/make/common/shared/Sanity.gmk
@@ -687,13 +687,13 @@
 ######################################################
 sane-alt_outputdir:
 ifdef ALT_OUTPUTDIR
- @if [ `$(ECHO) $(subst \,/,$(ALT_OUTPUTDIR)) | $(EGREP) -ci '^([a-z]:)?/'` -ne 1 ]; then \
+ @if [ `$(ECHO) $(subst \,/,$(ALT_OUTPUTDIR)) | $(EGREP) -c '^([A-Za-z]:)?/'` -ne 1 ]; then \
          $(ECHO) "ERROR: ALT_OUTPUTDIR must be an Absolute Path Name, \n" \
            " not a Relative Path Name. \n" \
            "" >> $(ERROR_FILE) ; \
        fi
   ifeq ($(PLATFORM), windows)
- @if [ `$(ECHO) $(subst \,/,$(ALT_OUTPUTDIR)) | $(EGREP) -ci '^([a-z]:)'` -ne 1 ]; then \
+ @if [ `$(ECHO) $(subst \,/,$(ALT_OUTPUTDIR)) | $(EGREP) -c '^([A-Za-z]:)'` -ne 1 ]; then \
          $(ECHO) "ERROR: On windows, ALT_OUTPUTDIR must contain the drive letter. \n" \
            "" >> $(ERROR_FILE) ; \
        fi
@@ -742,7 +742,7 @@
 ######################################################
 sane-alt_bootdir:
 ifdef ALT_BOOTDIR
- @if [ `$(ECHO) $(subst \,/,$(ALT_BOOTDIR)) | $(EGREP) -ci '^([a-z]:)?/'` -ne 1 ]; then \
+ @if [ `$(ECHO) $(subst \,/,$(ALT_BOOTDIR)) | $(EGREP) -c '^([A-Za-z]:)?/'` -ne 1 ]; then \
          $(ECHO) "ERROR: ALT_BOOTDIR must be an Absolute Path Name, \n" \
            " not a Relative Path Name. \n" \
            " The current value of ALT_BOOTDIR is \n" \
@@ -772,7 +772,7 @@
 ######################################################
 sane-local-bootdir:
 ifeq ($(PLATFORM), windows)
- @if [ `$(ECHO) $(BOOTDIR) | $(EGREP) -ci '^J:'` -ne 0 ]; then \
+ @if [ `$(ECHO) $(BOOTDIR) | $(EGREP) -c '^[jJ]:'` -ne 0 ]; then \
          $(ECHO) "WARNING: Your BOOTDIR is located on the J: drive. Often the J:\n" \
            " drive is mapped over a network. Using a mapped drive for\n" \
            " the BOOTDIR may significantly slow down the build process.\n" \
@@ -789,7 +789,7 @@
 ######################################################
 sane-cacerts:
   ifdef ALT_CACERTS_FILE
- @if [ `$(ECHO) $(subst \,/,$(ALT_CACERTS_FILE)) | $(EGREP) -ci '^([a-z]:)?/'` -ne 1 ]; then \
+ @if [ `$(ECHO) $(subst \,/,$(ALT_CACERTS_FILE)) | $(EGREP) -c '^([A-Za-z]:)?/'` -ne 1 ]; then \
          $(ECHO) "ERROR: ALT_CACERTS_FILE must be an Absolute Path Name, \n" \
            " not a Relative Path Name. \n" \
            " The current value of ALT_CACERTS_FILE is \n" \
@@ -1538,7 +1538,7 @@
 sane-mozilla:
 ifeq ($(ARCH_DATA_MODEL), 32)
   ifdef ALT_MOZILLA_HEADERS_PATH
- @if [ `$(ECHO) $(subst \,/,$(ALT_MOZILLA_HEADERS_PATH)) | $(EGREP) -ci '^([a-z]:)?/'` -ne 1 ]; then \
+ @if [ `$(ECHO) $(subst \,/,$(ALT_MOZILLA_HEADERS_PATH)) | $(EGREP) -c '^([A-Za-z]:)?/'` -ne 1 ]; then \
          $(ECHO) "ERROR: ALT_MOZILLA_HEADERS_PATH must be an Absolute Path Name, \n" \
            " not a Relative Path Name. \n" \
            " The current value of ALT_MOZILLA_HEADERS_PATH is \n" \