• Example of the issue

Emacs : GNU Emacs 25.2.1 (x86_64-apple-darwin16.4.0, Carbon Version 157 AppKit 1504.81)
of 2017-03-07
Package: Org mode version 9.0.5 (release_9.0.5-351-g0e0fda.dirty @ /Users/stacey/.emacs.d/org-mode/lisp/)

In this buffer the TODO keywords are FIXME and FIXED, as set by:

+SEQ_TODO: FIXME FIXED

+BEGIN: clocktable :maxlevel 4 :scope subtree :link t

+CAPTION: Clock summary at [2017-04-14 Fri 20:01]

| Headline | Time | | | |
|----------------------------------------------------------------------------------------------------------------+-----------+---------+---+---|
| Total time | 1h 9min | | | |
|----------------------------------------------------------------------------------------------------------------+-----------+---------+---+---|
| [[file:/tmp/test.org::Example%20of%20the%20issue][Example of the issue]] | 1h 9min | | | |
| _ [[file:/tmp/test.org::Test%20log][Test log]] | | 0h 4min | | |
| _ [[file:/tmp/test.org::Test%20log][FIXME Test log]] | | 1h 0min | | |
| _ [[file:/tmp/test.org::test%20with%20comment%20no%20to-do][COMMENT test with comment no to-do]] | | 0h 2min | | |
| _ [[file:/tmp/test.org::FIXME%20comment%20with%20to-do%20keyword][COMMENT FIXME comment with to-do keyword]] | | 0h 1min | | |
| _ [[file:/tmp/test.org::with%20a%20fraction][FIXME with a fraction]] | | 0h 1min | | |
| _ [[file:/tmp/test.org::with%20a%20percentage][FIXME with a percentage]] | | 0h 1min | | |

+END:

** Test log
:LOGBOOK:
CLOCK: [2017-04-11 Tue 23:20]--[2017-04-11 Tue 23:24] => 0:04
:END:
** FIXME Test log
:LOGBOOK:
CLOCK: [2017-04-11 Tue 22:20]--[2017-04-11 Tue 23:20] => 1:00
:END:

** COMMENT test with comment no to-do
:LOGBOOK:
CLOCK: [2017-04-14 Fri 17:29]--[2017-04-14 Fri 17:31] => 0:02
:END:
** COMMENT FIXME comment with to-do keyword
:LOGBOOK:
CLOCK: [2017-04-14 Fri 17:31]--[2017-04-14 Fri 17:32] => 0:01
:END:
** FIXME with a fraction [1/2]
:LOGBOOK:
CLOCK: [2017-04-14 Fri 17:42]--[2017-04-14 Fri 17:43] => 0:01
:END:
- [X] One
- [ ] two
** FIXME with a percentage [50%]
:LOGBOOK:
CLOCK: [2017-04-14 Fri 17:32]--[2017-04-14 Fri 17:33] => 0:01
:END:
- [ ] one
- [X] two

• Patch

Appears that change ebbc675bd9890c451ad01910fa2625fa78baac9b way back
in 9.0.1 needed to also modify org-clock.el, or at least when I revert
that change I get the behavior I'm used to back.

Below is a patch which modifies org-clock.el; Though I'm sure it can
be approved upon.

+BEGIN_EXAMPLE diff

diff --git a/lisp/org-clock.el b/lisp/org-clock.el
index 0973cc21b..3e30d20f8 100644
--- a/lisp/org-clock.el
+++ b/lisp/org-clock.el
@@ -2801,12 +2801,17 @@ TIME: The sum of all time spend in this tree, in minutes. This time
(- (match-end 1) (match-beginning 1))))
(<= level maxlevel))
(setq hdl (if (not link)
- (match-string 2)
+ (org-get-heading t t t t)
(org-make-link-string
(format "file:%s::%s"
(buffer-file-name)
(save-match-data
- (match-string 2)))
+ (org-make-org-heading-search-string
+ (replace-regexp-in-string
+ org-bracket-link-regexp
+ (lambda (m) (or (match-string 3 m)
+ (match-string 1 m)))
+ (org-get-heading t t t t)))))
(org-make-org-heading-search-string
(replace-regexp-in-string
org-bracket-link-regexp

+END_EXAMPLE