* 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