error message while reindexing

I'm getting the following while re-indexing:

Deleting /usr/local/spkg/resin-2.1.11/alt.java.io.FileImpl@5f1ae9:issues
message = Unable to delete file /usr/local/spkg/resin-2.1.11/alt.java.io.FileImpl@5f1ae9:issues
Deleting /usr/local/spkg/resin-2.1.11/alt.java.io.FileImpl@5f1ae9:comments
message = Unable to delete file /usr/local/spkg/resin-2.1.11/alt.java.io.FileImpl@5f1ae9:comments
2003-11-17 13:57:03,060 ERROR [atlassian.core.util.FileFactory] Unable to delete directory /apps/jira/WEB-INF/index

apparently the process when reindexing is to first delete the old index directories, then recreate them. the "delete" portion of this doesn't seem to be working.

a bit of local config info to help interpret the above:

the configured index path is "/apps/jira/WEB-INF/index". this is correct, and
shows up correctly in the database. also, JIRA seems to be running fine.

the app server (and thus the java process' PWD) is located in /usr/local/spkg/resin-2.1.1.