Nondeterministic behavior with glob
Please provide the following information. The more we know about your system and use case, the more easily and likely we can help.

### Description of the problem / feature request / question:

_If asking a question or requesting a feature, also tell us about the underlying problem you're trying to solve._

1. Include a nested workspace as a `local_repository`.
2. `glob` files within the nested workspace.
3. The glob will sometimes be empty under identical circumstances and sometimes not.

### If possible, provide a minimal example to reproduce the problem:
```
$ find
.
./WORKSPACE
./BUILD
./nested
./nested/foo.txt
./nested/WORKSPACE
./nested/BUILD
$ cat nested/*
$ cat WORKSPACE
local_repository(
    name = "nested",
    path = "nested",
)
$ cat BUILD
filegroup(
    name = "foo",
    srcs = ["nested/foo.txt"],
)

filegroup(
    name = "glob",
    srcs = glob(["nested/foo.txt"]),
)
```
```
$ bazel query :all --output=build
```
will sometimes produce:
```
# /path/to/BUILD:6:1
filegroup(
  name = "glob",
  srcs = [],
)

# /path/to/BUILD:1:1
filegroup(
  name = "foo",
  srcs = ["//:nested/foo.txt"],
)
```
and sometimes:
```
# /path/to/BUILD:6:1
filegroup(
  name = "glob",
  srcs = ["//:nested/foo.txt"],
)

# /path/to/BUILD:1:1
filegroup(
  name = "foo",
  srcs = ["//:nested/foo.txt"],
)
```
with no discernable difference in environment.
Though one result will persist for some time.

### Environment info
* Operating System: Ubuntu 14.04.5 LTS


* Bazel version (output of `bazel info release`): release 0.5.3


###  Have you found anything relevant by searching the web?
(e.g. [StackOverflow answers](http://stackoverflow.com/questions/tagged/bazel),
[GitHub issues](https://github.com/bazelbuild/bazel/issues),
email threads on the [`bazel-discuss`](https://groups.google.com/forum/#!forum/bazel-discuss) Google group)


### Anything else, information or logs or outputs that would be helpful?
(If they are large, please upload as attachment or provide link).
